rs7118388

Variant names:

• chr11-34432600-A-G
• rs7118388
• ENST00000724590.1:n.100+153A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-34432600-A-G
• chr11-34432600-A-T

Variant summary

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

The ENST00000724590.1(ENSG00000294594):​n.100+153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,864 control chromosomes in the GnomAD database, including 20,798 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 0.51 (20798 hom., cov: 31)
• Consequence: ENSG00000294594 ENST00000724590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 14 publications found

Genes affected

ENSG00000294594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724590.1. 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
	ENSG00000294594	ENST00000724590.1		n.100+153A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77965 AN: 151746 Hom.: 20761 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.514 AC: 78041 AN: 151864 Hom.: 20798 Cov.: 31 AF XY: 0.510 AC XY: 37865 AN XY: 74222

African (AFR) AF: 0.636 AC: 26338 AN: 41404

American (AMR) AF: 0.367 AC: 5599 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1754 AN: 5150

South Asian (SAS) AF: 0.339 AC: 1627 AN: 4802

European-Finnish (FIN) AF: 0.542 AC: 5716 AN: 10542

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33689 AN: 67934

Other (OTH) AF: 0.478 AC: 1006 AN: 2106

Alfa AF: 0.495 Hom.: 75838

Bravo AF: 0.506

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		1.3

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: rs7118388;

hg19: chr11-34454147;