rs17739675

Variant names:

• chr2-64267779-C-A
• rs17739675
• ENST00000717282.1:n.779+7430C>A

Variant summary

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

The ENST00000717282.1(ENSG00000288932):​n.779+7430C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,162 control chromosomes in the GnomAD database, including 1,176 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 0.12 (1176 hom., cov: 32)
• Consequence: ENSG00000288932 ENST00000717282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 10 publications found

Genes affected

ENSG00000288932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717282.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288932	ENST00000717282.1		n.779+7430C>A		intron	N/A
	ENSG00000288932	ENST00000717283.1		n.254+38139C>A		intron	N/A
	ENSG00000288932	ENST00000717284.1		n.211-23366C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18498 AN: 152044 Hom.: 1173 Cov.: 32

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.122 AC: 18517 AN: 152162 Hom.: 1176 Cov.: 32 AF XY: 0.122 AC XY: 9048 AN XY: 74378

African (AFR) AF: 0.0940 AC: 3903 AN: 41522

American (AMR) AF: 0.115 AC: 1759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.0613 AC: 317 AN: 5170

South Asian (SAS) AF: 0.119 AC: 572 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1838 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9652 AN: 67978

Other (OTH) AF: 0.105 AC: 221 AN: 2112

Alfa AF: 0.129 Hom.: 1841

Bravo AF: 0.116

Asia WGS AF: 0.0890 AC: 284 AN: 3178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.7
DANN	Benign	0.79
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs17739675; hg19: chr2-64494913;