rs1463694

Variant names:

• chr4-156349024-C-T
• rs1463694

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;