rs1463694

Variant names:

• chr4-156349024-C-T
• rs1463694
• ENST00000778470.1:n.393+14663C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000778470.1(ENSG00000301356):​n.393+14663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000301356 ENST00000778470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

ENSG00000301356 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778470.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000301356	ENST00000778470.1		n.393+14663C>T		intron	N/A
	ENSG00000301356	ENST00000778471.1		n.202+14663C>T		intron	N/A

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

African (AFR) AF: 0.0984 AC: 4086 AN: 41512

American (AMR) AF: 0.132 AC: 2014 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3468

East Asian (EAS) AF: 0.0514 AC: 266 AN: 5174

South Asian (SAS) AF: 0.185 AC: 894 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2026 AN: 10534

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12839 AN: 67910

Other (OTH) AF: 0.158 AC: 333 AN: 2108

Alfa AF: 0.170 Hom.: 968

Bravo AF: 0.147

Asia WGS AF: 0.112 AC: 388 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1463694; hg19: chr4-157270176;