rs1024008

Variant names:

• chr3-72629872-A-G
• rs1024008
• ENST00000747314.1:n.667+8574T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-72629872-A-G
• chr3-72629872-A-T

Variant summary

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

The ENST00000747314.1(ENSG00000297356):​n.667+8574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,134 control chromosomes in the GnomAD database, including 20,675 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 0.52 (20675 hom., cov: 33)
• Consequence: ENSG00000297356 ENST00000747314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 3 publications found

Genes affected

ENSG00000297356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377161	XR_940962.3	n.851+8574T>C		intron_variant	Intron 8 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297356	ENST00000747314.1	n.667+8574T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78808 AN: 152016 Hom.: 20649 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.518 AC: 78879 AN: 152134 Hom.: 20675 Cov.: 33 AF XY: 0.523 AC XY: 38889 AN XY: 74380

African (AFR) AF: 0.543 AC: 22533 AN: 41520

American (AMR) AF: 0.568 AC: 8693 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3305 AN: 5160

South Asian (SAS) AF: 0.628 AC: 3031 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4874 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32727 AN: 67984

Other (OTH) AF: 0.527 AC: 1112 AN: 2110

Alfa AF: 0.424 Hom.: 1896

Bravo AF: 0.523

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.71
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1024008; hg19: chr3-72679023;