rs17642476

Variant names:

• chr17-45579014-G-C
• rs17642476
• ENST00000686949.1:n.134+5558C>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000686949.1(ENSG00000291175):​n.134+5558C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 149,226 control chromosomes in the GnomAD database, including 33 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 0.044 (33 hom., cov: 52)
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 6 publications found

Genes affected

ENSG00000291175 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High Homozygotes in GnomAd4 at 33 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686949.1. 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
	ENSG00000291175	ENST00000686949.1		n.134+5558C>G		intron	N/A
	ENSG00000291175	ENST00000701132.2		n.134+5558C>G		intron	N/A
	ENSG00000291175	ENST00000717223.1		n.560+6688C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6496 AN: 149110 Hom.: 33 Cov.: 52

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0265

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.0314

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0415

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

GnomAD4 genome AF: 0.0436 AC: 6500 AN: 149226 Hom.: 33 Cov.: 52 AF XY: 0.0458 AC XY: 3339 AN XY: 72976

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0109 AC: 452 AN: 41444

American (AMR) AF: 0.0666 AC: 998 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.0332 AC: 112 AN: 3378

East Asian (EAS) AF: 0.0701 AC: 361 AN: 5152

South Asian (SAS) AF: 0.0312 AC: 147 AN: 4708

European-Finnish (FIN) AF: 0.0942 AC: 969 AN: 10286

Middle Eastern (MID) AF: 0.0414 AC: 12 AN: 290

European-Non Finnish (NFE) AF: 0.0505 AC: 3334 AN: 66004

Other (OTH) AF: 0.0440 AC: 91 AN: 2070

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0607 Hom.: 4

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs17642476; hg19: chr17-43656380;