rs11020107

Variant names:

• chr11-92934564-G-C
• rs11020107
• ENST00000532770.2:n.146+3558G>C

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+3558G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,960 control chromosomes in the GnomAD database, including 9,826 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 0.36 (9826 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 10 publications found

Genes affected

ENSG00000254874 (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 (EAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000254874	ENST00000532770.2	n.146+3558G>C		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.128+3558G>C		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.115+3558G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54045 AN: 151842 Hom.: 9826 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.356 AC: 54075 AN: 151960 Hom.: 9826 Cov.: 32 AF XY: 0.358 AC XY: 26593 AN XY: 74258

African (AFR) AF: 0.383 AC: 15868 AN: 41448

American (AMR) AF: 0.286 AC: 4372 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1216 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2162 AN: 5140

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4816

European-Finnish (FIN) AF: 0.421 AC: 4445 AN: 10548

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22825 AN: 67942

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.351 Hom.: 1155

Bravo AF: 0.346

Asia WGS AF: 0.350 AC: 1218 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	1.9
DANN	Benign	0.35
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11020107; hg19: chr11-92667730;