rs971732

Variant names:

• chr2-49914979-A-C
• rs971732

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 0.392 in 151,942 control chromosomes in the GnomAD database, including 11,910 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 0.39 (11910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 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: 0.392 AC: 59487 AN: 151824 Hom.: 11897 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.392 AC: 59544 AN: 151942 Hom.: 11910 Cov.: 32 AF XY: 0.395 AC XY: 29324 AN XY: 74246

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.397

Alfa AF: 0.370 Hom.: 19822

Bravo AF: 0.398

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971732; hg19: chr2-50142117;