rs4659007

Variant names:

• chr1-119503863-T-A
• rs4659007
• ENST00000632456.2:n.243-13751A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-119503863-T-A
• chr1-119503863-T-G

Variant summary

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

The ENST00000632456.2(ENSG00000293080):​n.243-13751A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,910 control chromosomes in the GnomAD database, including 43,467 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 0.75 (43467 hom., cov: 30)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 4 publications found

Genes affected

ENSG00000293080 (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 = 0.901 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
ENSG00000293080	ENST00000632456.2	n.243-13751A>T		intron_variant	Intron 2 of 6	6
ENSG00000293080	ENST00000756941.1	n.219-18255A>T		intron_variant	Intron 2 of 2
ENSG00000293080	ENST00000756942.1	n.259-13751A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113683 AN: 151790 Hom.: 43422 Cov.: 30

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.749 AC: 113787 AN: 151910 Hom.: 43467 Cov.: 30 AF XY: 0.757 AC XY: 56192 AN XY: 74212

African (AFR) AF: 0.879 AC: 36457 AN: 41470

American (AMR) AF: 0.781 AC: 11926 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3468

East Asian (EAS) AF: 0.923 AC: 4773 AN: 5172

South Asian (SAS) AF: 0.826 AC: 3976 AN: 4812

European-Finnish (FIN) AF: 0.736 AC: 7688 AN: 10452

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44236 AN: 67960

Other (OTH) AF: 0.718 AC: 1514 AN: 2110

Alfa AF: 0.602 Hom.: 1682

Bravo AF: 0.757

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.60
DANN	Benign	0.61
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4659007; hg19: chr1-120046486; COSMIC: COSV52489902;