15-61532102-A-C

Position:

• chr15-61532102-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000559783.2(ENSG00000259616):​n.124-24862T>G 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 0.625 in 151,874 control chromosomes in the GnomAD database, including 29,643 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 0.62 (29643 hom., cov: 31)
• Consequence: ENST00000559783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984782	XR_001751569.2	n.236-24862T>G		intron_variant, non_coding_transcript_variant
LOC107984782	XR_001751570.2	n.221-24862T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559783.2	n.124-24862T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94794 AN: 151756 Hom.: 29616 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.625 AC: 94874 AN: 151874 Hom.: 29643 Cov.: 31 AF XY: 0.624 AC XY: 46335 AN XY: 74216

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.607

Alfa AF: 0.610 Hom.: 12928

Bravo AF: 0.631

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3935962; hg19: chr15-61824301;