rs17709344

chr15-93608310-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001751681.2(LOC107983974):n.1032+15577G>A variant causes a intron, non coding transcript 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: LOC107983974 XR_001751681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

Genes affected

LOC107983974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983974	XR_001751681.2	n.1032+15577G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554318.2	n.324+14951G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000653322.2	n.964+15577G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0977

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0354

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0436 Hom.: 126

Bravo AF: 0.0485

Asia WGS AF: 0.191 AC: 663 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.0
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17709344; hg19: chr15-94151539;