chr3-80215451-T-C

Variant names:

• chr3-80215451-T-C
• rs10511115

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 0.0682 in 152,220 control chromosomes in the GnomAD database, including 938 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 0.068 (938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.0681 AC: 10362 AN: 152102 Hom.: 932 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.00706

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00469

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0682 AC: 10388 AN: 152220 Hom.: 938 Cov.: 32 AF XY: 0.0670 AC XY: 4983 AN XY: 74422

African (AFR) AF: 0.198 AC: 8237 AN: 41498

American (AMR) AF: 0.0416 AC: 636 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3470

East Asian (EAS) AF: 0.170 AC: 880 AN: 5174

South Asian (SAS) AF: 0.0145 AC: 70 AN: 4830

European-Finnish (FIN) AF: 0.00706 AC: 75 AN: 10620

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00469 AC: 319 AN: 68030

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0307 Hom.: 130

Bravo AF: 0.0775

Asia WGS AF: 0.121 AC: 421 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	3.0
DANN	Benign	0.66
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10511115; hg19: chr3-80264601;