rs276865

Positions:

• chr15-39264234-G-A

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.67+156675C>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 0.545 in 151,692 control chromosomes in the GnomAD database, including 26,564 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 0.54 (26564 hom., cov: 30)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+156310C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.67+156675C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+95555C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000561058.5	n.44+9606C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000664681.1	n.41+9606C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82531 AN: 151574 Hom.: 26494 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.545 AC: 82664 AN: 151692 Hom.: 26564 Cov.: 30 AF XY: 0.543 AC XY: 40259 AN XY: 74112

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.510

Alfa AF: 0.449 Hom.: 3647

Bravo AF: 0.578

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276865; hg19: chr15-39556435;