rs17884563

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986822	XR_007060439.1	n.557+3687T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233942	ENST00000718462.1	n.589+3687T>A		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818771.1	n.521+3687T>A		intron_variant	Intron 1 of 8
ENSG00000233942	ENST00000818772.1	n.463+3687T>A		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1	n.435+3687T>A		intron_variant	Intron 1 of 5

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 v4.3

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;