7-81170518-T-G

Variant names:

• chr7-81170518-T-G
• rs500454
• ENST00000719862.1:n.139-16096A>C

Variant summary

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

The ENST00000719862.1(ENSG00000289996):​n.139-16096A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 152,050 control chromosomes in the GnomAD database, including 74,516 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 0.99 (74516 hom., cov: 31)
• Consequence: ENSG00000289996 ENST00000719862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 2 publications found

Genes affected

ENSG00000289996 (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 = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719862.1. 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
	ENSG00000289996	ENST00000719862.1		n.139-16096A>C		intron	N/A
	ENSG00000237896	ENST00000720000.1		n.130+1882T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150402 AN: 151932 Hom.: 74459 Cov.: 31

Gnomad AFR AF: 0.999

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.990 AC: 150518 AN: 152050 Hom.: 74516 Cov.: 31 AF XY: 0.988 AC XY: 73435 AN XY: 74316

African (AFR) AF: 0.999 AC: 41456 AN: 41516

American (AMR) AF: 0.997 AC: 15203 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3424 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5153 AN: 5156

South Asian (SAS) AF: 0.947 AC: 4566 AN: 4824

European-Finnish (FIN) AF: 0.966 AC: 10238 AN: 10594

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67213 AN: 67930

Other (OTH) AF: 0.992 AC: 2091 AN: 2108

Alfa AF: 0.989 Hom.: 31999

Bravo AF: 0.994

Asia WGS AF: 0.979 AC: 3405 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	3.8
DANN	Benign	0.77
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs500454; hg19: chr7-80799834;