chr1-60447414-T-C

Variant names:

• chr1-60447414-T-C
• rs1501229
• ENST00000794751.1:n.392+42714A>G

Variant summary

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

The ENST00000794751.1(ENSG00000303463):​n.392+42714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 151,928 control chromosomes in the GnomAD database, including 67,046 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 0.94 (67046 hom., cov: 31)
• Consequence: ENSG00000303463 ENST00000794751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 1 publications found

Genes affected

ENSG00000303463 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000303463	ENST00000794751.1	n.392+42714A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142377 AN: 151810 Hom.: 67016 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.938 AC: 142459 AN: 151928 Hom.: 67046 Cov.: 31 AF XY: 0.938 AC XY: 69712 AN XY: 74294

African (AFR) AF: 0.845 AC: 35054 AN: 41476

American (AMR) AF: 0.966 AC: 14730 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3418 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5171 AN: 5172

South Asian (SAS) AF: 0.949 AC: 4580 AN: 4826

European-Finnish (FIN) AF: 0.969 AC: 10267 AN: 10592

Middle Eastern (MID) AF: 0.973 AC: 284 AN: 292

European-Non Finnish (NFE) AF: 0.974 AC: 66073 AN: 67826

Other (OTH) AF: 0.949 AC: 2003 AN: 2110

Alfa AF: 0.941 Hom.: 3531

Bravo AF: 0.934

Asia WGS AF: 0.968 AC: 3331 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.41
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1501229; hg19: chr1-60913086;