chr15-34078286-T-C

Variant names:

• chr15-34078286-T-C
• rs2705338

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 0.773 in 152,104 control chromosomes in the GnomAD database, including 45,751 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 0.77 (45751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117453 AN: 151986 Hom.: 45713 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.773 AC: 117550 AN: 152104 Hom.: 45751 Cov.: 32 AF XY: 0.774 AC XY: 57549 AN XY: 74362

African (AFR) AF: 0.723 AC: 29962 AN: 41464

American (AMR) AF: 0.770 AC: 11772 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2194 AN: 3466

East Asian (EAS) AF: 0.965 AC: 4999 AN: 5180

South Asian (SAS) AF: 0.869 AC: 4190 AN: 4822

European-Finnish (FIN) AF: 0.755 AC: 7991 AN: 10578

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53872 AN: 67988

Other (OTH) AF: 0.767 AC: 1619 AN: 2110

Alfa AF: 0.790 Hom.: 27942

Bravo AF: 0.770

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2705338; hg19: chr15-34370487;