rs703361

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000288172 (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 (AMR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000672708.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288172	ENST00000672708.1		n.73+2383C>T		intron	N/A

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

African (AFR) AF: 0.647 AC: 26778 AN: 41412

American (AMR) AF: 0.820 AC: 12521 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2732 AN: 3466

East Asian (EAS) AF: 0.758 AC: 3895 AN: 5140

South Asian (SAS) AF: 0.637 AC: 3067 AN: 4812

European-Finnish (FIN) AF: 0.805 AC: 8504 AN: 10564

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55007 AN: 68002

Other (OTH) AF: 0.801 AC: 1691 AN: 2110

Alfa AF: 0.793 Hom.: 199871

Bravo AF: 0.758

Asia WGS AF: 0.716 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.60
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs703361;

hg19: chr10-119341820;