11-128871844-T-C

Variant names:

• chr11-128871844-T-C
• rs7116606

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 0.7 in 152,078 control chromosomes in the GnomAD database, including 37,506 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 0.70 (37506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.700 AC: 106433 AN: 151960 Hom.: 37467 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.700 AC: 106515 AN: 152078 Hom.: 37506 Cov.: 33 AF XY: 0.705 AC XY: 52435 AN XY: 74346

African (AFR) AF: 0.639 AC: 26479 AN: 41428

American (AMR) AF: 0.774 AC: 11837 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2374 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4292 AN: 5182

South Asian (SAS) AF: 0.639 AC: 3084 AN: 4824

European-Finnish (FIN) AF: 0.736 AC: 7786 AN: 10578

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48252 AN: 67982

Other (OTH) AF: 0.701 AC: 1481 AN: 2114

Alfa AF: 0.709 Hom.: 58578

Bravo AF: 0.699

Asia WGS AF: 0.740 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7116606; hg19: chr11-128741739;