4-15935015-C-T

Position:

• chr4-15935015-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0882 in 152,268 control chromosomes in the GnomAD database, including 895 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 0.088 (895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13435 AN: 152150 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0882 AC: 13429 AN: 152268 Hom.: 895 Cov.: 32 AF XY: 0.0902 AC XY: 6718 AN XY: 74452

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0974

Alfa AF: 0.0975 Hom.: 634

Bravo AF: 0.0918

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12499618; hg19: chr4-15936638;