rs957749

Variant names:

• chr2-210755857-A-G
• rs957749

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 0.259 in 151,910 control chromosomes in the GnomAD database, including 5,271 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 0.26 (5271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 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: 0.259 AC: 39280 AN: 151790 Hom.: 5266 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.259 AC: 39307 AN: 151910 Hom.: 5271 Cov.: 32 AF XY: 0.255 AC XY: 18938 AN XY: 74220

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.276

Alfa AF: 0.287 Hom.: 3105

Bravo AF: 0.258

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957749; hg19: chr2-211620581;