rs11856995

Positions:

• chr15-95782414-T-C

Variant summary

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

The ENST00000612595.2(ENSG00000275016):​n.284-42775T>C 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 0.23 in 152,110 control chromosomes in the GnomAD database, including 4,851 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 (4851 hom., cov: 32)
• Consequence: ENST00000612595.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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.284-42775T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34987 AN: 151990 Hom.: 4850 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.230 AC: 34998 AN: 152110 Hom.: 4851 Cov.: 32 AF XY: 0.226 AC XY: 16840 AN XY: 74364

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.265

Alfa AF: 0.288 Hom.: 13463

Bravo AF: 0.227

Asia WGS AF: 0.187 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11856995; hg19: chr15-96325643;