rs703361

Variant names:

• chr10-117582309-C-T
• rs703361
• ENST00000672708.1:n.73+2383C>T

Variant summary

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

The ENST00000672708.1(ENSG00000288172):​n.73+2383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 151,980 control chromosomes in the GnomAD database, including 44,211 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 0.76 (44211 hom., cov: 31)
• Consequence: ENSG00000288172 ENST00000672708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

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 (AMR) allele frequency at 95% confidence interval = 0.808 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.73+2383C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115041 AN: 151862 Hom.: 44151 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.758 AC: 115164 AN: 151980 Hom.: 44211 Cov.: 31 AF XY: 0.757 AC XY: 56228 AN XY: 74254

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.801

Alfa AF: 0.799 Hom.: 96992

Bravo AF: 0.758

Asia WGS AF: 0.716 AC: 2492 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	4.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703361; hg19: chr10-119341820;