rs1463694

chr4-156349024-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 0.153 in 151,958 control chromosomes in the GnomAD database, including 1,934 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 0.15 (1934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 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: 0.153 AC: 23178 AN: 151840 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.153 AC: 23197 AN: 151958 Hom.: 1934 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74250

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0514

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.158

Alfa AF: 0.169 Hom.: 633

Bravo AF: 0.147

Asia WGS AF: 0.112 AC: 388 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.39
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463694; hg19: chr4-157270176;