rs1520195

Variant names:

• chr3-184019094-G-A
• rs1520195

Your query was ambiguous. Multiple possible variants found:

• chr3-184019094-G-A
• chr3-184019094-G-C

Variant summary

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

The variant allele was found at a frequency of 0.566 in 152,042 control chromosomes in the GnomAD database, including 25,320 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 0.57 (25320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85931 AN: 151924 Hom.: 25275 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.566 AC: 86033 AN: 152042 Hom.: 25320 Cov.: 32 AF XY: 0.560 AC XY: 41651 AN XY: 74316

African (AFR) AF: 0.722 AC: 29962 AN: 41486

American (AMR) AF: 0.540 AC: 8256 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1767 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3981 AN: 5172

South Asian (SAS) AF: 0.518 AC: 2499 AN: 4820

European-Finnish (FIN) AF: 0.407 AC: 4290 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33480 AN: 67950

Other (OTH) AF: 0.573 AC: 1210 AN: 2112

Alfa AF: 0.509 Hom.: 4120

Bravo AF: 0.582

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.40
DANN	Benign	0.93
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1520195; hg19: chr3-183736882;