11-71269860-C-T

Variant names:

• chr11-71269860-C-T
• rs10897897

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 0.342 in 152,070 control chromosomes in the GnomAD database, including 9,056 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 0.34 (9056 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51925 AN: 151952 Hom.: 9049 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.342 AC: 51966 AN: 152070 Hom.: 9056 Cov.: 33 AF XY: 0.344 AC XY: 25545 AN XY: 74318

African (AFR) AF: 0.312 AC: 12919 AN: 41468

American (AMR) AF: 0.381 AC: 5829 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3464

East Asian (EAS) AF: 0.431 AC: 2229 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2330 AN: 4818

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10570

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22821 AN: 67976

Other (OTH) AF: 0.342 AC: 721 AN: 2110

Alfa AF: 0.343 Hom.: 36223

Bravo AF: 0.344

Asia WGS AF: 0.457 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10897897; hg19: chr11-70980906;