11-71269860-C-T

Variant names:

• chr11-71269860-C-T
• rs10897897

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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.342 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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.342

Alfa AF: 0.345 Hom.: 16654

Bravo AF: 0.344

Asia WGS AF: 0.457 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10897897; hg19: chr11-70980906;