rs11020124

Variant names:

• chr11-92957495-T-C
• rs11020124
• ENST00000532770.2:n.147-2730T>C

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.147-2730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,922 control chromosomes in the GnomAD database, including 7,840 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 0.32 (7840 hom., cov: 31)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 14 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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.147-2730T>C		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.129-2730T>C		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.116-2730T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48245 AN: 151804 Hom.: 7839 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.318 AC: 48273 AN: 151922 Hom.: 7840 Cov.: 31 AF XY: 0.320 AC XY: 23756 AN XY: 74236

African (AFR) AF: 0.359 AC: 14871 AN: 41442

American (AMR) AF: 0.234 AC: 3568 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2300 AN: 5154

South Asian (SAS) AF: 0.387 AC: 1861 AN: 4804

European-Finnish (FIN) AF: 0.355 AC: 3743 AN: 10532

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19812 AN: 67950

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.301 Hom.: 10658

Bravo AF: 0.309

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11020124; hg19: chr11-92690661; COSMIC: COSV107158818;