rs17709344

Variant names:

• chr15-93608310-G-A
• rs17709344
• ENST00000554318.2:n.324+14951G>A

Variant summary

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

The ENST00000554318.2(ENSG00000257060):​n.324+14951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,152 control chromosomes in the GnomAD database, including 331 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 (331 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 7 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554318.2. 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
	ENSG00000257060	ENST00000554318.2	TSL:3	n.324+14951G>A		intron	N/A
	ENSG00000257060	ENST00000653322.2		n.964+15577G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6709 AN: 152034 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0442 AC: 6723 AN: 152152 Hom.: 331 Cov.: 32 AF XY: 0.0472 AC XY: 3510 AN XY: 74398

African (AFR) AF: 0.0119 AC: 492 AN: 41510

American (AMR) AF: 0.0977 AC: 1494 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.187 AC: 966 AN: 5170

South Asian (SAS) AF: 0.161 AC: 774 AN: 4804

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10598

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2406 AN: 68000

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0418 Hom.: 158

Bravo AF: 0.0485

Asia WGS AF: 0.191 AC: 663 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.34
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs17709344; hg19: chr15-94151539;