rs1919481

Positions:

• chr2-61824389-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM161A	XM_047445962.1	c.1838+2715C>T		intron_variant			XP_047301918.1
		n.61824389G>A		intergenic_region
FAM161A	XR_001738972.3	n.2025+2715C>T		intron_variant
FAM161A	XR_007082540.1	n.2025+2715C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.372

Alfa AF: 0.344 Hom.: 15783

Bravo AF: 0.365

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919481; hg19: chr2-62051524;