rs956053

Variant names:

• chr3-10981140-G-A
• rs956053

Your query was ambiguous. Multiple possible variants found:

• chr3-10981140-G-A
• chr3-10981140-G-C
• chr3-10981140-G-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 0.223 in 151,290 control chromosomes in the GnomAD database, including 4,510 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 0.22 (4510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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: 0.223 AC: 33778 AN: 151174 Hom.: 4515 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.223 AC: 33774 AN: 151290 Hom.: 4510 Cov.: 32 AF XY: 0.226 AC XY: 16687 AN XY: 73906

African (AFR) AF: 0.0716 AC: 2940 AN: 41040

American (AMR) AF: 0.284 AC: 4313 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3464

East Asian (EAS) AF: 0.248 AC: 1273 AN: 5142

South Asian (SAS) AF: 0.356 AC: 1703 AN: 4780

European-Finnish (FIN) AF: 0.231 AC: 2430 AN: 10500

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18917 AN: 67862

Other (OTH) AF: 0.251 AC: 528 AN: 2104

Alfa AF: 0.267 Hom.: 18410

Bravo AF: 0.217

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs956053; hg19: chr3-11022826;