rs72958776

Variant names:

• chr2-120357660-C-A
• rs72958776

Your query was ambiguous. Multiple possible variants found:

• chr2-120357660-C-A
• chr2-120357660-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 0.0763 in 152,176 control chromosomes in the GnomAD database, including 707 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 0.076 (707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.0761 AC: 11577 AN: 152058 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0763 AC: 11607 AN: 152176 Hom.: 707 Cov.: 32 AF XY: 0.0744 AC XY: 5537 AN XY: 74410

African (AFR) AF: 0.171 AC: 7106 AN: 41480

American (AMR) AF: 0.0499 AC: 763 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 224 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4824

European-Finnish (FIN) AF: 0.0219 AC: 233 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2845 AN: 67996

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0263 Hom.: 20

Bravo AF: 0.0829

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs72958776; hg19: chr2-121115236;