rs11047543

Variant names:

• chr12-24635405-G-A
• rs11047543
• ENST00000741714.1:n.372-17595C>T

Variant summary

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

The ENST00000741714.1(ENSG00000296761):​n.372-17595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,788 control chromosomes in the GnomAD database, including 1,307 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 (1307 hom., cov: 32)
• Consequence: ENSG00000296761 ENST00000741714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 43 publications found

Genes affected

ENSG00000296761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741714.1. 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
	ENSG00000296761	ENST00000741714.1		n.372-17595C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18172 AN: 151670 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.120 AC: 18181 AN: 151788 Hom.: 1307 Cov.: 32 AF XY: 0.120 AC XY: 8936 AN XY: 74200

African (AFR) AF: 0.0406 AC: 1683 AN: 41464

American (AMR) AF: 0.163 AC: 2473 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3462

East Asian (EAS) AF: 0.128 AC: 660 AN: 5160

South Asian (SAS) AF: 0.256 AC: 1231 AN: 4810

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9965 AN: 67780

Other (OTH) AF: 0.148 AC: 312 AN: 2106

Alfa AF: 0.142 Hom.: 4765

Bravo AF: 0.120

Asia WGS AF: 0.191 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		0.013

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: rs11047543;

hg19: chr12-24788339;