rs1157916

chr10-113543984-G-Achr10-113543984-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;