ENST00000741164.1:n.174+10276G>A

Variant names:

• chr7-4444798-G-A
• rs314593
• ENST00000741164.1:n.174+10276G>A

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.174+10276G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,036 control chromosomes in the GnomAD database, including 63,285 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 0.91 (63285 hom., cov: 33)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 publications found

Genes affected

ENSG00000296681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741164.1. 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
	ENSG00000296681	ENST00000741164.1		n.174+10276G>A		intron	N/A
	ENSG00000296681	ENST00000741167.1		n.214+10276G>A		intron	N/A
	ENSG00000296681	ENST00000741168.1		n.254+10276G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138437 AN: 151918 Hom.: 63242 Cov.: 33

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.911 AC: 138538 AN: 152036 Hom.: 63285 Cov.: 33 AF XY: 0.908 AC XY: 67448 AN XY: 74320

African (AFR) AF: 0.936 AC: 38814 AN: 41476

American (AMR) AF: 0.842 AC: 12862 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3251 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4099 AN: 5150

South Asian (SAS) AF: 0.844 AC: 4061 AN: 4812

European-Finnish (FIN) AF: 0.912 AC: 9650 AN: 10576

Middle Eastern (MID) AF: 0.911 AC: 266 AN: 292

European-Non Finnish (NFE) AF: 0.923 AC: 62717 AN: 67956

Other (OTH) AF: 0.918 AC: 1940 AN: 2114

Alfa AF: 0.916 Hom.: 79272

Bravo AF: 0.907

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.37
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs314593; hg19: chr7-4484429;