rs11858157

Variant names:

• chr15-91852168-A-G
• rs11858157
• ENST00000761994.1:n.94+1918T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761994.1(ENSG00000299260):​n.94+1918T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,990 control chromosomes in the GnomAD database, including 5,228 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 0.25 (5228 hom., cov: 32)
• Consequence: ENSG00000299260 ENST00000761994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 2 publications found

Genes affected

ENSG00000299260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 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
ENSG00000299260	ENST00000761994.1	n.94+1918T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37837 AN: 151872 Hom.: 5219 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.249 AC: 37880 AN: 151990 Hom.: 5228 Cov.: 32 AF XY: 0.243 AC XY: 18065 AN XY: 74322

African (AFR) AF: 0.368 AC: 15233 AN: 41420

American (AMR) AF: 0.219 AC: 3343 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.0184 AC: 95 AN: 5170

South Asian (SAS) AF: 0.108 AC: 518 AN: 4818

European-Finnish (FIN) AF: 0.171 AC: 1814 AN: 10598

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15158 AN: 67924

Other (OTH) AF: 0.242 AC: 508 AN: 2102

Alfa AF: 0.232 Hom.: 1512

Bravo AF: 0.258

Asia WGS AF: 0.0960 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs11858157; hg19: chr15-92395398;