15-39239112-T-C

Position:

• chr15-39239112-T-C

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.68-167504A>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 0.499 in 151,448 control chromosomes in the GnomAD database, including 19,584 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 0.50 (19584 hom., cov: 31)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370777	XR_007064588.1	n.518-167504A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560484.1	n.68-167504A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+120677A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000561058.5	n.44+34728A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000664681.1	n.41+34728A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75566 AN: 151330 Hom.: 19564 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.499 AC: 75648 AN: 151448 Hom.: 19584 Cov.: 31 AF XY: 0.498 AC XY: 36860 AN XY: 73966

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.453

Alfa AF: 0.443 Hom.: 22266

Bravo AF: 0.507

Asia WGS AF: 0.445 AC: 1544 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276855; hg19: chr15-39531313;