rs1919481

Variant names:

• chr2-61824389-G-A
• rs1919481
• XM_047445962.1:c.1838+2715C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047445962.1(FAM161A):​c.1838+2715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,622 control chromosomes in the GnomAD database, including 10,757 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10757 hom., cov: 30)
• Consequence: FAM161A XM_047445962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 3 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55184 AN: 151506 Hom.: 10735 Cov.: 30

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55237 AN: 151622 Hom.: 10757 Cov.: 30 AF XY: 0.376 AC XY: 27809 AN XY: 74054

African (AFR) AF: 0.308 AC: 12726 AN: 41322

American (AMR) AF: 0.490 AC: 7448 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3466

East Asian (EAS) AF: 0.680 AC: 3510 AN: 5164

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4806

European-Finnish (FIN) AF: 0.441 AC: 4620 AN: 10466

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22676 AN: 67892

Other (OTH) AF: 0.372 AC: 784 AN: 2110

Alfa AF: 0.345 Hom.: 26268

Bravo AF: 0.365

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1919481; hg19: chr2-62051524;