ENST00000751594.1:n.485-633A>G

Variant names:

• chr10-113962652-A-G
• rs180940
• ENST00000751594.1:n.485-633A>G

Variant summary

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

The ENST00000751594.1(ENSG00000297898):​n.485-633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,462 control chromosomes in the GnomAD database, including 31,397 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 0.64 (31397 hom., cov: 28)
• Consequence: ENSG00000297898 ENST00000751594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 6 publications found

Genes affected

ENSG00000297898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 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
ENSG00000297898	ENST00000751594.1	n.485-633A>G		intron_variant	Intron 2 of 3
ENSG00000297898	ENST00000751595.1	n.228-633A>G		intron_variant	Intron 1 of 2
ENSG00000297898	ENST00000751596.1	n.78-1956A>G		intron_variant	Intron 1 of 1
ENSG00000297898	ENST00000751600.1	n.126+3655A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96707 AN: 151346 Hom.: 31370 Cov.: 28

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.639 AC: 96787 AN: 151462 Hom.: 31397 Cov.: 28 AF XY: 0.646 AC XY: 47818 AN XY: 73984

African (AFR) AF: 0.555 AC: 22881 AN: 41258

American (AMR) AF: 0.650 AC: 9894 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1874 AN: 3466

East Asian (EAS) AF: 0.480 AC: 2458 AN: 5120

South Asian (SAS) AF: 0.687 AC: 3284 AN: 4780

European-Finnish (FIN) AF: 0.795 AC: 8323 AN: 10470

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 45911 AN: 67844

Other (OTH) AF: 0.609 AC: 1283 AN: 2108

Alfa AF: 0.653 Hom.: 12466

Bravo AF: 0.620

Asia WGS AF: 0.559 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs180940; hg19: chr10-115722411;