rs11856995

Variant names:

• chr15-95782414-T-C
• rs11856995
• ENST00000612595.2:n.284-42775T>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 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: ENSG00000275016 ENST00000612595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

ENSG00000275016 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275016	ENST00000612595.2	n.284-42775T>C		intron_variant	Intron 2 of 2	5
ENSG00000275016	ENST00000616588.4	n.251-27665T>C		intron_variant	Intron 2 of 3	5
ENSG00000275016	ENST00000656202.1	n.235-42775T>C		intron_variant	Intron 3 of 3

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;