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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.297 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

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.319

Alfa AF: 0.313 Hom.: 1673

Bravo AF: 0.277

Asia WGS AF: 0.244 AC: 852 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	0.023
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7901053; hg19: chr10-50803542;