10-114029616-C-T

Variant names:

• chr10-114029616-C-T
• rs7076938
• ENST00000729868.1:n.343-6981G>A

Variant summary

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

The ENST00000729868.1(ENSG00000295421):​n.343-6981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,046 control chromosomes in the GnomAD database, including 37,211 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 0.70 (37211 hom., cov: 31)
• Consequence: ENSG00000295421 ENST00000729868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 33 publications found

Genes affected

ENSG00000295421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729868.1. 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
	ENSG00000295421	ENST00000729868.1		n.343-6981G>A		intron	N/A
	ENSG00000295421	ENST00000729869.1		n.125-6981G>A		intron	N/A
	ENSG00000295421	ENST00000729870.1		n.233+1838G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105703 AN: 151928 Hom.: 37169 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.696 AC: 105803 AN: 152046 Hom.: 37211 Cov.: 31 AF XY: 0.699 AC XY: 51944 AN XY: 74308

African (AFR) AF: 0.600 AC: 24862 AN: 41464

American (AMR) AF: 0.767 AC: 11722 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2131 AN: 3464

East Asian (EAS) AF: 0.762 AC: 3949 AN: 5180

South Asian (SAS) AF: 0.743 AC: 3570 AN: 4806

European-Finnish (FIN) AF: 0.746 AC: 7880 AN: 10570

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49533 AN: 67966

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.716 Hom.: 111141

Bravo AF: 0.691

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.038

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: rs7076938;

hg19: chr10-115789375;