11-80305092-T-C

Variant names:

• chr11-80305092-T-C
• rs10501461

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 0.0659 in 152,174 control chromosomes in the GnomAD database, including 425 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 0.066 (425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.149 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: 0.0659 AC: 10013 AN: 152056 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0659 AC: 10024 AN: 152174 Hom.: 425 Cov.: 32 AF XY: 0.0689 AC XY: 5128 AN XY: 74376

African (AFR) AF: 0.0293 AC: 1217 AN: 41556

American (AMR) AF: 0.0621 AC: 948 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3470

East Asian (EAS) AF: 0.158 AC: 811 AN: 5132

South Asian (SAS) AF: 0.111 AC: 538 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5019 AN: 67986

Other (OTH) AF: 0.0614 AC: 130 AN: 2116

Alfa AF: 0.0735 Hom.: 360

Bravo AF: 0.0646

Asia WGS AF: 0.107 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.37
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10501461; hg19: chr11-80016136;