10-121208012-C-T

Variant names:

• chr10-121208012-C-T
• rs10749408
• ENST00000718585.1:n.67-9794G>A

Variant summary

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

The ENST00000718585.1(ENSG00000293725):​n.67-9794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,086 control chromosomes in the GnomAD database, including 39,965 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 0.72 (39965 hom., cov: 32)
• Consequence: ENSG00000293725 ENST00000718585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 11 publications found

Genes affected

ENSG00000293725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718585.1. 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
	ENSG00000293725	ENST00000718585.1		n.67-9794G>A		intron	N/A
	ENSG00000293725	ENST00000718586.1		n.247-14402G>A		intron	N/A
	ENSG00000293725	ENST00000718587.1		n.246-9794G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109751 AN: 151966 Hom.: 39896 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.723 AC: 109887 AN: 152086 Hom.: 39965 Cov.: 32 AF XY: 0.723 AC XY: 53758 AN XY: 74330

African (AFR) AF: 0.797 AC: 33087 AN: 41494

American (AMR) AF: 0.764 AC: 11686 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2323 AN: 3468

East Asian (EAS) AF: 0.704 AC: 3637 AN: 5168

South Asian (SAS) AF: 0.635 AC: 3057 AN: 4816

European-Finnish (FIN) AF: 0.673 AC: 7108 AN: 10558

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46746 AN: 67982

Other (OTH) AF: 0.701 AC: 1479 AN: 2110

Alfa AF: 0.704 Hom.: 18074

Bravo AF: 0.736

Asia WGS AF: 0.693 AC: 2408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.17
PhyloP100		-0.59

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: rs10749408;

hg19: chr10-122967526;