chr11-80177902-T-C

Variant names:

• chr11-80177902-T-C
• rs6591876

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 0.415 in 151,968 control chromosomes in the GnomAD database, including 13,775 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 0.41 (13775 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 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: 0.415 AC: 63050 AN: 151846 Hom.: 13773 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.415 AC: 63060 AN: 151968 Hom.: 13775 Cov.: 31 AF XY: 0.415 AC XY: 30851 AN XY: 74278

African (AFR) AF: 0.298 AC: 12360 AN: 41442

American (AMR) AF: 0.354 AC: 5408 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.331 AC: 1703 AN: 5146

South Asian (SAS) AF: 0.370 AC: 1780 AN: 4814

European-Finnish (FIN) AF: 0.482 AC: 5091 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.494 AC: 33567 AN: 67938

Other (OTH) AF: 0.423 AC: 892 AN: 2110

Alfa AF: 0.458 Hom.: 2048

Bravo AF: 0.400

Asia WGS AF: 0.321 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.84
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6591876; hg19: chr11-79888946; COSMIC: COSV69496188;