chr11-97866007-G-T

Variant names:

• chr11-97866007-G-T
• rs949175

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 0.295 in 151,584 control chromosomes in the GnomAD database, including 6,947 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 0.29 (6947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 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: 0.295 AC: 44674 AN: 151468 Hom.: 6941 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.295 AC: 44696 AN: 151584 Hom.: 6947 Cov.: 32 AF XY: 0.293 AC XY: 21684 AN XY: 74040

African (AFR) AF: 0.218 AC: 9033 AN: 41388

American (AMR) AF: 0.263 AC: 3993 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3464

East Asian (EAS) AF: 0.152 AC: 782 AN: 5154

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3856 AN: 10468

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.345 AC: 23400 AN: 67800

Other (OTH) AF: 0.335 AC: 701 AN: 2094

Alfa AF: 0.337 Hom.: 12598

Bravo AF: 0.289

Asia WGS AF: 0.184 AC: 637 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs949175; hg19: chr11-97737007; COSMIC: COSV51267247;