10-117590250-C-T

Variant names:

• chr10-117590250-C-T
• rs71003
• ENST00000672708.1:n.294+746C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000672708.1(ENSG00000288172):​n.294+746C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 149,644 control chromosomes in the GnomAD database, including 27,849 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 0.61 (27849 hom., cov: 25)
• Consequence: ENSG00000288172 ENST00000672708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

Genes affected

ENSG00000288172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 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
ENSG00000288172	ENST00000672708.1	n.294+746C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.609 AC: 91130 AN: 149530 Hom.: 27806 Cov.: 25

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.610 AC: 91240 AN: 149644 Hom.: 27849 Cov.: 25 AF XY: 0.615 AC XY: 44746 AN XY: 72816

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.580

Alfa AF: 0.595 Hom.: 36081

Bravo AF: 0.600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71003; hg19: chr10-119349761;