rs11135876

Variant names:

• chr8-25619866-C-T
• rs11135876
• ENST00000670669.1:n.131-10309C>T

Variant summary

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

The ENST00000670669.1(ENSG00000253100):​n.131-10309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,910 control chromosomes in the GnomAD database, including 6,855 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 0.27 (6855 hom., cov: 33)
• Consequence: ENSG00000253100 ENST00000670669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 1 publications found

Genes affected

ENSG00000253100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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
ENSG00000253100	ENST00000670669.1	n.131-10309C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40762 AN: 151792 Hom.: 6831 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.269 AC: 40845 AN: 151910 Hom.: 6855 Cov.: 33 AF XY: 0.270 AC XY: 20025 AN XY: 74250

African (AFR) AF: 0.482 AC: 19965 AN: 41414

American (AMR) AF: 0.186 AC: 2839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 855 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1543 AN: 5166

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10550

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11070 AN: 67900

Other (OTH) AF: 0.223 AC: 469 AN: 2106

Alfa AF: 0.193 Hom.: 9545

Bravo AF: 0.273

Asia WGS AF: 0.300 AC: 1044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs11135876; hg19: chr8-25477382;