7-113419590-C-T

Variant names:

• chr7-113419590-C-T
• rs2894673
• ENST00000724069.1:n.441-27974G>A

Variant summary

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

The ENST00000724069.1(ENSG00000294519):​n.441-27974G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,124 control chromosomes in the GnomAD database, including 25,855 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 0.58 (25855 hom., cov: 29)
• Consequence: ENSG00000294519 ENST00000724069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• Publications: 3 publications found

Genes affected

ENSG00000294519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724069.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294519	ENST00000724069.1		n.441-27974G>A		intron	N/A
	ENSG00000294519	ENST00000724070.1		n.128-27974G>A		intron	N/A
	ENSG00000294519	ENST00000724071.1		n.359+2404G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87603 AN: 151006 Hom.: 25822 Cov.: 29

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.580 AC: 87689 AN: 151124 Hom.: 25855 Cov.: 29 AF XY: 0.581 AC XY: 42874 AN XY: 73734

African (AFR) AF: 0.605 AC: 24879 AN: 41138

American (AMR) AF: 0.592 AC: 8989 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1812 AN: 3460

East Asian (EAS) AF: 0.917 AC: 4697 AN: 5124

South Asian (SAS) AF: 0.648 AC: 3099 AN: 4784

European-Finnish (FIN) AF: 0.538 AC: 5562 AN: 10338

Middle Eastern (MID) AF: 0.569 AC: 165 AN: 290

European-Non Finnish (NFE) AF: 0.545 AC: 36981 AN: 67812

Other (OTH) AF: 0.598 AC: 1249 AN: 2090

Alfa AF: 0.553 Hom.: 2928

Bravo AF: 0.585

Asia WGS AF: 0.779 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2894673; hg19: chr7-113059645;