rs1606520

Variant names:

• chr3-164468661-G-A
• rs1606520
• ENST00000701346.1:n.258+17126G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-164468661-G-A
• chr3-164468661-G-T

Variant summary

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

The ENST00000701346.1(ENSG00000289884):​n.258+17126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,878 control chromosomes in the GnomAD database, including 19,280 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 0.50 (19280 hom., cov: 31)
• Consequence: ENSG00000289884 ENST00000701346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

Genes affected

ENSG00000289884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374191	XR_001740998.2	n.290+17126G>A		intron_variant	Intron 1 of 3
LOC105374191	XR_001740999.3	n.290+17126G>A		intron_variant	Intron 1 of 3
LOC105374191	XR_001741000.2	n.290+17126G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289884	ENST00000701346.1	n.258+17126G>A		intron_variant	Intron 1 of 5
ENSG00000289884	ENST00000702159.2	n.302+17126G>A		intron_variant	Intron 1 of 3
ENSG00000289884	ENST00000721983.1	n.84+17904G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75894 AN: 151760 Hom.: 19252 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.500 AC: 75971 AN: 151878 Hom.: 19280 Cov.: 31 AF XY: 0.499 AC XY: 37047 AN XY: 74212

African (AFR) AF: 0.574 AC: 23790 AN: 41438

American (AMR) AF: 0.557 AC: 8479 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1620 AN: 3462

East Asian (EAS) AF: 0.344 AC: 1769 AN: 5140

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4820

European-Finnish (FIN) AF: 0.511 AC: 5388 AN: 10544

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31434 AN: 67930

Other (OTH) AF: 0.488 AC: 1025 AN: 2102

Alfa AF: 0.385 Hom.: 1154

Bravo AF: 0.510

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1606520; hg19: chr3-164186449;