15-95644576-C-T

Position:

• chr15-95644576-C-T

Variant summary

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

The ENST00000612595.2(ENSG00000275016):​n.204+6057C>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 0.226 in 151,916 control chromosomes in the GnomAD database, including 3,987 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 0.23 (3987 hom., cov: 32)
• Consequence: ENST00000612595.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000612595.2	n.204+6057C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34281 AN: 151798 Hom.: 3978 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.226 AC: 34316 AN: 151916 Hom.: 3987 Cov.: 32 AF XY: 0.225 AC XY: 16729 AN XY: 74236

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.240

Alfa AF: 0.216 Hom.: 5250

Bravo AF: 0.231

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	6.1
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: rs17504636; hg19: chr15-96187805;