Genetic Variant FAM161A:n.*2313dupA (chr2-61825639-C-CT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000456262.5(FAM161A):n.*2313dupA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0827 in 375,228 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 31)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

FAM161A
ENST00000456262.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

Publications

0 publications found

Variant links:

Genes affected

FAM161A (HGNC:25808): (FAM161 centrosomal protein A) This gene belongs to the FAM161 family. It is expressed mainly in the retina. Mouse studies suggested that this gene is involved in development of retinal progenitors during embryogenesis, and that its activity is restricted to mature photoreceptors after birth. Mutations in this gene cause autosomal recessive retinitis pigmentosa-28. Alternatively spliced transcript variants have been identified.[provided by RefSeq, Jan 2011]

FAM161A Gene-Disease associations (from GenCC):

retinitis pigmentosa 28
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
retinitis pigmentosa
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

FAM161A links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM161A	NM_001201543.2 link	c.*815dupA		3_prime_UTR_variant	Exon 7 of 7	ENST00000404929.6	NP_001188472.1	Q3B820-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM161A	ENST00000404929.6 link	c.*815dupA		3_prime_UTR_variant	Exon 7 of 7	1	NM_001201543.2	ENSP00000385158.1		Q3B820-3

Frequencies

GnomAD3 genomes

AF:

0.00104

AC:

147

AN:

141776

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000899

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00114

Gnomad ASJ

AF:

0.000299

Gnomad EAS

AF:

0.000202

Gnomad SAS

AF:

0.00202

Gnomad FIN

AF:

0.00283

Gnomad MID

AF:

0.00680

Gnomad NFE

AF:

0.000869

Gnomad OTH

AF:

0.00159

GnomAD2 exomes

AF:

0.173

AC:

8806

AN:

50930

AF XY:

0.168

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.184

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.213

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.177

GnomAD4 exome

AF:

0.132

AC:

30899

AN:

233464

Hom.:

Cov.:

AF XY:

0.134

AC XY:

17991

AN XY:

134438

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.148

AC:

797

AN:

5390

American (AMR)

AF:

0.129

AC:

2036

AN:

15838

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

971

AN:

8192

East Asian (EAS)

AF:

0.153

AC:

1207

AN:

7906

South Asian (SAS)

AF:

0.130

AC:

5856

AN:

45056

European-Finnish (FIN)

AF:

0.118

AC:

1131

AN:

9610

Middle Eastern (MID)

AF:

0.119

AC:

AN:

800

European-Non Finnish (NFE)

AF:

0.134

AC:

17355

AN:

129770

Other (OTH)

AF:

0.133

AC:

1451

AN:

10902

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.276

Heterozygous variant carriers

2731

5463

8194

10926

13657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00104

AC:

148

AN:

141764

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

68702

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000949

AC:

AN:

39002

American (AMR)

AF:

0.00114

AC:

AN:

14072

Ashkenazi Jewish (ASJ)

AF:

0.000299

AC:

AN:

3344

East Asian (EAS)

AF:

0.000202

AC:

AN:

4942

South Asian (SAS)

AF:

0.00180

AC:

AN:

4440

European-Finnish (FIN)

AF:

0.00283

AC:

AN:

8480

Middle Eastern (MID)

AF:

0.00741

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.000869

AC:

AN:

64430

Other (OTH)

AF:

0.00159

AC:

AN:

1890

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.380

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0277

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-61825639-CTTTTTTT-CTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over