rs13373771

Variant names:

• chr1-152471132-C-A
• rs13373771

Your query was ambiguous. Multiple possible variants found:

• chr1-152471132-C-A
• chr1-152471132-C-G
• chr1-152471132-C-T

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 0.52 in 152,050 control chromosomes in the GnomAD database, including 21,188 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 0.52 (21188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.520 AC: 79044 AN: 151932 Hom.: 21165 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.520 AC: 79097 AN: 152050 Hom.: 21188 Cov.: 32 AF XY: 0.525 AC XY: 39056 AN XY: 74338

African (AFR) AF: 0.376 AC: 15584 AN: 41460

American (AMR) AF: 0.553 AC: 8454 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3047 AN: 5162

South Asian (SAS) AF: 0.514 AC: 2480 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6929 AN: 10576

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38921 AN: 67958

Other (OTH) AF: 0.552 AC: 1167 AN: 2116

Alfa AF: 0.557 Hom.: 8566

Bravo AF: 0.505

Asia WGS AF: 0.520 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.77
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs13373771; hg19: chr1-152443608; COSMIC: COSV52826546;