rs17691914

Variant names:

• chr3-34921311-A-G
• rs17691914
• ENST00000726556.1:n.222+225A>G

Variant summary

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

The ENST00000726556.1(ENSG00000294886):​n.222+225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0628 in 152,298 control chromosomes in the GnomAD database, including 428 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 0.063 (428 hom., cov: 33)
• Consequence: ENSG00000294886 ENST00000726556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 1 publications found

Genes affected

ENSG00000294886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726556.1. 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
	LOC101928135	NR_110817.1		n.207-41845T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294886	ENST00000726556.1		n.222+225A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 9555 AN: 152180 Hom.: 424 Cov.: 33

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0628 AC: 9568 AN: 152298 Hom.: 428 Cov.: 33 AF XY: 0.0643 AC XY: 4788 AN XY: 74474

African (AFR) AF: 0.0181 AC: 753 AN: 41576

American (AMR) AF: 0.0754 AC: 1152 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5176

South Asian (SAS) AF: 0.0998 AC: 482 AN: 4828

European-Finnish (FIN) AF: 0.0874 AC: 928 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0790 AC: 5377 AN: 68024

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.0757 Hom.: 78

Bravo AF: 0.0604

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.67
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs17691914; hg19: chr3-34962803;