rs117020818

Variant names:

• chr11-13107616-G-A
• rs117020818
• ENST00000531136.1:n.47+27177C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-13107616-G-A
• chr11-13107616-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000531136.1(ENSG00000255558):​n.47+27177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 152,044 control chromosomes in the GnomAD database, including 55 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 0.022 (55 hom., cov: 32)
• Consequence: ENSG00000255558 ENST00000531136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 1 publications found

Genes affected

ENSG00000255558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0217 (3295/152044) while in subpopulation AMR AF = 0.0393 (600/15260). AF 95% confidence interval is 0.0367. There are 55 homozygotes in GnomAd4. There are 1567 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 55 gene

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
ENSG00000255558	ENST00000531136.1	n.47+27177C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0217 AC: 3293 AN: 151926 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.00583

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00520

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0321

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0217 AC: 3295 AN: 152044 Hom.: 55 Cov.: 32 AF XY: 0.0211 AC XY: 1567 AN XY: 74332

African (AFR) AF: 0.00581 AC: 241 AN: 41480

American (AMR) AF: 0.0393 AC: 600 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.00521 AC: 25 AN: 4802

European-Finnish (FIN) AF: 0.0152 AC: 161 AN: 10586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0321 AC: 2183 AN: 67962

Other (OTH) AF: 0.0209 AC: 44 AN: 2108

Alfa AF: 0.0211 Hom.: 22

Bravo AF: 0.0224

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.66
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs117020818; hg19: chr11-13129163;