rs2973062

Variant names:

• chr5-37788387-C-T
• rs2973062

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 0.449 in 151,958 control chromosomes in the GnomAD database, including 15,614 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 0.45 (15614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.449 AC: 68249 AN: 151840 Hom.: 15607 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.449 AC: 68293 AN: 151958 Hom.: 15614 Cov.: 32 AF XY: 0.443 AC XY: 32919 AN XY: 74274

African (AFR) AF: 0.504 AC: 20871 AN: 41418

American (AMR) AF: 0.388 AC: 5934 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1630 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1532 AN: 4808

European-Finnish (FIN) AF: 0.392 AC: 4137 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31243 AN: 67936

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.457 Hom.: 2241

Bravo AF: 0.452

Asia WGS AF: 0.314 AC: 1094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2973062; hg19: chr5-37788489;