11-94199552-C-G

Variant names:

• chr11-94199552-C-G
• rs4753547
• ENST00000733243.1:n.194G>C

Variant summary

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

The ENST00000733243.1(ENSG00000295858):​n.194G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,128 control chromosomes in the GnomAD database, including 1,355 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 0.12 (1355 hom., cov: 32)
• Consequence: ENSG00000295858 ENST00000733243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 3 publications found

Genes affected

ENSG00000295858 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733243.1. 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
	ENSG00000295858	ENST00000733243.1		n.194G>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000250519	ENST00000655054.1		n.320+10469C>G		intron	N/A
	ENSG00000250519	ENST00000733069.1		n.491+10469C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18908 AN: 152010 Hom.: 1355 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.124 AC: 18912 AN: 152128 Hom.: 1355 Cov.: 32 AF XY: 0.126 AC XY: 9364 AN XY: 74366

African (AFR) AF: 0.0524 AC: 2174 AN: 41524

American (AMR) AF: 0.171 AC: 2620 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3466

East Asian (EAS) AF: 0.0538 AC: 278 AN: 5166

South Asian (SAS) AF: 0.0995 AC: 478 AN: 4804

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10663 AN: 67970

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.141 Hom.: 209

Bravo AF: 0.123

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		0.33

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: rs4753547;

hg19: chr11-93932718;