rs2414739

chr15-61701935-G-A

Variant summary

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

The ENST00000662958.3(ENSG00000259675):n.89+13180C>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 0.674 in 152,004 control chromosomes in the GnomAD database, including 35,240 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 0.67 (35240 hom., cov: 32)
• Consequence: ENST00000662958.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

(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 = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984782	XR_001751569.2	n.72+13180C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662958.3	n.89+13180C>T		intron_variant, non_coding_transcript_variant
	ENST00000559590.2	n.61+13180C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000691967.2	n.80+13180C>T		intron_variant, non_coding_transcript_variant
	ENST00000700958.1	n.44+13180C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102358 AN: 151886 Hom.: 35228 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.674 AC: 102420 AN: 152004 Hom.: 35240 Cov.: 32 AF XY: 0.672 AC XY: 49939 AN XY: 74290

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.731

Alfa AF: 0.730 Hom.: 88060

Bravo AF: 0.678

Asia WGS AF: 0.736 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.28
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2414739; hg19: chr15-61994134;