rs2414718

Positions:

• chr15-61570934-G-A
• chr15-61570934-G-C
• chr15-61570934-G-T

Variant summary

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

The ENST00000559783.2(ENSG00000259616):​n.123+18982C>T 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 0.527 in 151,980 control chromosomes in the GnomAD database, including 21,652 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 0.53 (21652 hom., cov: 32)
• Consequence: ENST00000559783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984782	XR_001751569.2	n.235+18982C>T		intron_variant, non_coding_transcript_variant
LOC107984782	XR_001751570.2	n.220+18982C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559783.2	n.123+18982C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80034 AN: 151862 Hom.: 21648 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.527 AC: 80058 AN: 151980 Hom.: 21652 Cov.: 32 AF XY: 0.527 AC XY: 39139 AN XY: 74272

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.545

Alfa AF: 0.563 Hom.: 12660

Bravo AF: 0.516

Asia WGS AF: 0.541 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2414718; hg19: chr15-61863133;