rs1157916

Variant names:

• chr10-113543984-G-A
• rs1157916

Your query was ambiguous. Multiple possible variants found:

• chr10-113543984-G-A
• chr10-113543984-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 0.262 in 152,152 control chromosomes in the GnomAD database, including 6,606 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 (6606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 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: 0.262 AC: 39838 AN: 152034 Hom.: 6611 Cov.: 33

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.262 AC: 39827 AN: 152152 Hom.: 6606 Cov.: 33 AF XY: 0.262 AC XY: 19448 AN XY: 74364

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.227

Alfa AF: 0.189 Hom.: 443

Bravo AF: 0.237

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1157916; hg19: chr10-115303743;