rs11194701

Variant names:

• chr10-109532698-T-G
• rs11194701

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 0.486 in 151,116 control chromosomes in the GnomAD database, including 18,642 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 0.49 (18642 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 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: 0.486 AC: 73410 AN: 151000 Hom.: 18627 Cov.: 30

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.486 AC: 73460 AN: 151116 Hom.: 18642 Cov.: 30 AF XY: 0.479 AC XY: 35349 AN XY: 73820

African (AFR) AF: 0.333 AC: 13716 AN: 41144

American (AMR) AF: 0.541 AC: 8214 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3464

East Asian (EAS) AF: 0.518 AC: 2660 AN: 5134

South Asian (SAS) AF: 0.336 AC: 1613 AN: 4796

European-Finnish (FIN) AF: 0.444 AC: 4585 AN: 10334

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39054 AN: 67750

Other (OTH) AF: 0.487 AC: 1024 AN: 2104

Alfa AF: 0.533 Hom.: 2722

Bravo AF: 0.487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11194701; hg19: chr10-111292456; COSMIC: COSV70459378;