11-121333892-A-G

Variant names:

• chr11-121333892-A-G
• rs4936613
• ENST00000761170.1:n.329-20721T>C

Variant summary

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

The ENST00000761170.1(ENSG00000299150):​n.329-20721T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,214 control chromosomes in the GnomAD database, including 60,042 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 0.89 (60042 hom., cov: 32)
• Consequence: ENSG00000299150 ENST00000761170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 5 publications found

Genes affected

ENSG00000299150 (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 (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761170.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299150	ENST00000761170.1		n.329-20721T>C		intron	N/A
	ENSG00000299150	ENST00000761171.1		n.384+567T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134960 AN: 152096 Hom.: 59989 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.887 AC: 135073 AN: 152214 Hom.: 60042 Cov.: 32 AF XY: 0.887 AC XY: 65962 AN XY: 74404

African (AFR) AF: 0.934 AC: 38793 AN: 41538

American (AMR) AF: 0.903 AC: 13800 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3118 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4724 AN: 5184

South Asian (SAS) AF: 0.861 AC: 4154 AN: 4824

European-Finnish (FIN) AF: 0.844 AC: 8931 AN: 10584

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58569 AN: 68010

Other (OTH) AF: 0.880 AC: 1862 AN: 2116

Alfa AF: 0.881 Hom.: 11164

Bravo AF: 0.896

Asia WGS AF: 0.882 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.50
PhyloP100		-0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4936613;

hg19: chr11-121204601;