rs17881071

Variant names:

• chr7-95402152-G-A
• rs17881071
• ENST00000718462.1:n.589+5124G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-95402152-G-A
• chr7-95402152-G-C
• chr7-95402152-G-T

Variant summary

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

The ENST00000718462.1(ENSG00000233942):​n.589+5124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,948 control chromosomes in the GnomAD database, including 3,712 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 0.19 (3712 hom., cov: 31)
• Consequence: ENSG00000233942 ENST00000718462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233942	ENST00000718462.1		n.589+5124G>A		intron	N/A
	ENSG00000233942	ENST00000818771.1		n.521+5124G>A		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.463+5124G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29147 AN: 151830 Hom.: 3707 Cov.: 31

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.192 AC: 29162 AN: 151948 Hom.: 3712 Cov.: 31 AF XY: 0.198 AC XY: 14732 AN XY: 74224

African (AFR) AF: 0.0945 AC: 3916 AN: 41444

American (AMR) AF: 0.334 AC: 5097 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3238 AN: 5162

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1612 AN: 10500

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12757 AN: 67976

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.197 Hom.: 4491

Bravo AF: 0.206

Asia WGS AF: 0.407 AC: 1412 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.62
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs17881071; hg19: chr7-95031464;