chr10-5291045-G-A

Variant names:

• chr10-5291045-G-A
• rs7076488
• ENST00000744973.1:n.142+663C>T

Variant summary

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

The ENST00000744973.1(ENSG00000291045):​n.142+663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,084 control chromosomes in the GnomAD database, including 30,855 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 0.63 (30855 hom., cov: 32)
• Consequence: ENSG00000291045 ENST00000744973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 6 publications found

Genes affected

ENSG00000291045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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
ENSG00000291045	ENST00000744973.1	n.142+663C>T		intron_variant	Intron 1 of 8
ENSG00000291045	ENST00000744974.1	n.107+751C>T		intron_variant	Intron 1 of 5
ENSG00000291045	ENST00000744975.1	n.190+663C>T		intron_variant	Intron 1 of 5
ENSG00000291045	ENST00000744982.1	n.100+663C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96163 AN: 151966 Hom.: 30821 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.633 AC: 96255 AN: 152084 Hom.: 30855 Cov.: 32 AF XY: 0.636 AC XY: 47256 AN XY: 74344

African (AFR) AF: 0.706 AC: 29270 AN: 41480

American (AMR) AF: 0.573 AC: 8761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3909 AN: 5170

South Asian (SAS) AF: 0.752 AC: 3628 AN: 4826

European-Finnish (FIN) AF: 0.599 AC: 6333 AN: 10580

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40249 AN: 67946

Other (OTH) AF: 0.607 AC: 1283 AN: 2114

Alfa AF: 0.604 Hom.: 82565

Bravo AF: 0.630

Asia WGS AF: 0.768 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.72
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7076488; hg19: chr10-5333008;