Genetic Variant FAM161A:n.*2312_*2313dupAA (chr2-61825639-C-CTT) – 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.*2312_*2313dupAA 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 0.00125 in 397,562 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 0.000028 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0019 ( 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.814_815dupAA		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.814_815dupAA		3_prime_UTR_variant	Exon 7 of 7	1	NM_001201543.2	ENSP00000385158.1		Q3B820-3

Frequencies

GnomAD3 genomes

AF:

0.0000282

AC:

AN:

141814

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000711

Gnomad ASJ

AF:

0.000299

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000236

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00424

AC:

216

AN:

50930

AF XY:

0.00446

show subpopulations

Gnomad AFR exome

AF:

0.00156

Gnomad AMR exome

AF:

0.00400

Gnomad ASJ exome

AF:

0.00472

Gnomad EAS exome

AF:

0.00450

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00452

Gnomad OTH exome

AF:

0.00592

GnomAD4 exome

AF:

0.00193

AC:

493

AN:

255760

Hom.:

Cov.:

AF XY:

0.00204

AC XY:

300

AN XY:

147264

show subpopulations

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

African (AFR)

AF:

0.00223

AC:

AN:

5828

American (AMR)

AF:

0.00297

AC:

AN:

16832

Ashkenazi Jewish (ASJ)

AF:

0.00207

AC:

AN:

8708

East Asian (EAS)

AF:

0.00273

AC:

AN:

8792

South Asian (SAS)

AF:

0.00218

AC:

108

AN:

49494

European-Finnish (FIN)

AF:

0.000758

AC:

AN:

10548

Middle Eastern (MID)

AF:

0.00115

AC:

AN:

872

European-Non Finnish (NFE)

AF:

0.00171

AC:

244

AN:

142768

Other (OTH)

AF:

0.00227

AC:

AN:

11918

⚠️ 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: 0.260

Heterozygous variant carriers

126

190

253

316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000282

AC:

AN:

141802

Hom.:

Cov.:

AF XY:

0.0000291

AC XY:

AN XY:

68730

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

39000

American (AMR)

AF:

0.0000710

AC:

AN:

14078

Ashkenazi Jewish (ASJ)

AF:

0.000299

AC:

AN:

3344

East Asian (EAS)

AF:

0.00

AC:

AN:

4942

South Asian (SAS)

AF:

0.00

AC:

AN:

4442

European-Finnish (FIN)

AF:

0.000236

AC:

AN:

8484

Middle Eastern (MID)

AF:

0.00

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64458

Other (OTH)

AF:

0.00

AC:

AN:

1890

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00142

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

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

Publications

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2-61825639-CTTTTTTT-CTTTTTTTTT

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