chr15-34713685-T-A

Position:

• chr15-34713685-T-A

Variant summary

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

The variant allele was found at a frequency of 0.498 in 152,108 control chromosomes in the GnomAD database, including 19,181 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 (19181 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

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 (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34713685T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75643 AN: 151990 Hom.: 19169 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.498 AC: 75691 AN: 152108 Hom.: 19181 Cov.: 32 AF XY: 0.491 AC XY: 36539 AN XY: 74382

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.492

Alfa AF: 0.486 Hom.: 2245

Bravo AF: 0.506

Asia WGS AF: 0.530 AC: 1845 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	0.19
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: rs524952; hg19: chr15-35005886;