15-94968608-A-G

Position:

• chr15-94968608-A-G

Variant summary

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

The ENST00000615751.4(ENSG00000293024):​n.75-52436A>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 0.457 in 152,012 control chromosomes in the GnomAD database, including 16,606 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 0.46 (16606 hom., cov: 32)
• Consequence: ENST00000615751.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000615751.4	n.75-52436A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69436 AN: 151894 Hom.: 16570 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.457 AC: 69516 AN: 152012 Hom.: 16606 Cov.: 32 AF XY: 0.449 AC XY: 33340 AN XY: 74318

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.443

Alfa AF: 0.449 Hom.: 22762

Bravo AF: 0.462

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6496074; hg19: chr15-95511837;