rs7901053

Variant names:

• chr10-49595496-G-A
• rs7901053

Your query was ambiguous. Multiple possible variants found:

• chr10-49595496-G-A
• chr10-49595496-G-C
• chr10-49595496-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 0.296 in 151,844 control chromosomes in the GnomAD database, including 8,394 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 0.30 (8394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45035 AN: 151726 Hom.: 8398 Cov.: 31

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.296 AC: 45015 AN: 151844 Hom.: 8394 Cov.: 31 AF XY: 0.293 AC XY: 21730 AN XY: 74176

African (AFR) AF: 0.0762 AC: 3157 AN: 41442

American (AMR) AF: 0.284 AC: 4335 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1119 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1161 AN: 5134

South Asian (SAS) AF: 0.241 AC: 1151 AN: 4774

European-Finnish (FIN) AF: 0.395 AC: 4156 AN: 10532

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28701 AN: 67924

Other (OTH) AF: 0.319 AC: 672 AN: 2104

Alfa AF: 0.306 Hom.: 1676

Bravo AF: 0.277

Asia WGS AF: 0.244 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.023
DANN	Benign	0.67
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7901053; hg19: chr10-50803542;