rs7112939

Variant names:

• chr11-80322367-C-T
• rs7112939
• ENST00000532605.1:n.79-241G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532605.1(ENSG00000254434):​n.79-241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 151,874 control chromosomes in the GnomAD database, including 851 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 0.047 (851 hom., cov: 32)
• Consequence: ENSG00000254434 ENST00000532605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

ENSG00000254434 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254434	ENST00000532605.1	n.79-241G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7162 AN: 151756 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.00465

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00359

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0472 AC: 7170 AN: 151874 Hom.: 851 Cov.: 32 AF XY: 0.0534 AC XY: 3961 AN XY: 74192

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.00465

Gnomad4 NFE AF: 0.00359

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0244 Hom.: 48

Bravo AF: 0.0647

Asia WGS AF: 0.197 AC: 683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7112939; hg19: chr11-80033411;