rs2894895

Positions:

• chr15-95099447-T-G

Variant summary

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

The ENST00000615751.4(ENSG00000293024):​n.435-23478T>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 0.172 in 152,110 control chromosomes in the GnomAD database, including 2,558 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 0.17 (2558 hom., cov: 32)
• Consequence: ENST00000615751.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370991	XR_002957693.2	n.488-23478T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000615751.4	n.435-23478T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000658436.1	n.187-7177A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26155 AN: 151990 Hom.: 2554 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.172 AC: 26180 AN: 152110 Hom.: 2558 Cov.: 32 AF XY: 0.176 AC XY: 13052 AN XY: 74360

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.216

Alfa AF: 0.170 Hom.: 4672

Bravo AF: 0.185

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
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: rs2894895; hg19: chr15-95642676;