rs11197672

Variant names:

• chr10-116413959-A-G
• rs11197672

Your query was ambiguous. Multiple possible variants found:

• chr10-116413959-A-G
• chr10-116413959-A-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 0.325 in 152,106 control chromosomes in the GnomAD database, including 14,443 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 0.33 (14443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.325 AC: 49336 AN: 151988 Hom.: 14392 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.0760

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.325 AC: 49458 AN: 152106 Hom.: 14443 Cov.: 32 AF XY: 0.324 AC XY: 24108 AN XY: 74340

African (AFR) AF: 0.758 AC: 31426 AN: 41460

American (AMR) AF: 0.386 AC: 5889 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0760 AC: 264 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2380 AN: 5160

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4818

European-Finnish (FIN) AF: 0.121 AC: 1278 AN: 10596

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6930 AN: 68008

Other (OTH) AF: 0.290 AC: 614 AN: 2114

Alfa AF: 0.250 Hom.: 8677

Bravo AF: 0.373

Asia WGS AF: 0.336 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.78
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs11197672; hg19: chr10-118173471;