chr7-95400715-T-A

Variant names:

• chr7-95400715-T-A
• rs17884563
• ENST00000718462.1:n.589+3687T>A

Variant summary

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

The ENST00000718462.1(ENSG00000233942):​n.589+3687T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,038 control chromosomes in the GnomAD database, including 471 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 0.068 (471 hom., cov: 31)
• Consequence: ENSG00000233942 ENST00000718462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718462.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233942	ENST00000718462.1		n.589+3687T>A		intron	N/A
	ENSG00000233942	ENST00000818771.1		n.521+3687T>A		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.463+3687T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10336 AN: 151920 Hom.: 473 Cov.: 31

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0680 AC: 10332 AN: 152038 Hom.: 471 Cov.: 31 AF XY: 0.0661 AC XY: 4912 AN XY: 74278

African (AFR) AF: 0.0173 AC: 719 AN: 41476

American (AMR) AF: 0.0736 AC: 1122 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.126 AC: 648 AN: 5144

South Asian (SAS) AF: 0.0805 AC: 387 AN: 4808

European-Finnish (FIN) AF: 0.0456 AC: 483 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0933 AC: 6344 AN: 67988

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0773 Hom.: 76

Bravo AF: 0.0695

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs17884563; hg19: chr7-95030027;