rs156658

chr15-39243175-G-Achr15-39243175-G-Cchr15-39243175-G-T

Variant summary

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

The ENST00000560484.1(ENSG00000259345):n.68-171567C>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 0.869 in 152,060 control chromosomes in the GnomAD database, including 57,703 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 0.87 (57703 hom., cov: 31)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370777	XR_007064588.1	n.518-171567C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560484.1	n.68-171567C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+116614C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000561058.5	n.44+30665C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000664681.1	n.41+30665C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132098 AN: 151942 Hom.: 57673 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.869 AC: 132187 AN: 152060 Hom.: 57703 Cov.: 31 AF XY: 0.874 AC XY: 64955 AN XY: 74308

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.862

Alfa AF: 0.888 Hom.: 76859

Bravo AF: 0.862

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs156658; hg19: chr15-39535376;