Genetic Variant FAM161A:c.*815dupA (chr2-61825639-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001201543.2(FAM161A):c.*815dupA variant causes a 3 prime UTR 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
NM_001201543.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

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 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

GnomAD4 exome

AF:

0.132

AC:

30899

AN:

233464

Hom.:

Cov.:

AF XY:

0.134

AC XY:

17991

AN XY:

134438

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.119

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.133

GnomAD4 genome

AF:

0.00104

AC:

148

AN:

141764

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

68702

show subpopulations

Gnomad4 AFR

AF:

0.000949

Gnomad4 AMR

AF:

0.00114

Gnomad4 ASJ

AF:

0.000299

Gnomad4 EAS

AF:

0.000202

Gnomad4 SAS

AF:

0.00180

Gnomad4 FIN

AF:

0.00283

Gnomad4 NFE

AF:

0.000869

Gnomad4 OTH

AF:

0.00159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

2-61825639-CTTTTTTT-CTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over