rs2973062

Variant names:

• chr5-37788387-C-T
• rs2973062

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.467

Alfa AF: 0.455 Hom.: 2138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2973062; hg19: chr5-37788489;