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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.159+153A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294594	ENST00000724590.1	n.100+153A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7118388; hg19: chr11-34454147;