11-112127040-G-C

Variant names:

• chr11-112127040-G-C
• rs4937075
• ENST00000532699.1:n.314+38029G>C

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.314+38029G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,988 control chromosomes in the GnomAD database, including 41,466 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 0.74 (41466 hom., cov: 30)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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
ENSG00000255292	ENST00000532699.1	n.314+38029G>C		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.319+38029G>C		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.314+38029G>C		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111983 AN: 151870 Hom.: 41396 Cov.: 30

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.738 AC: 112118 AN: 151988 Hom.: 41466 Cov.: 30 AF XY: 0.741 AC XY: 55076 AN XY: 74286

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.741

Alfa AF: 0.722 Hom.: 4665

Bravo AF: 0.741

Asia WGS AF: 0.824 AC: 2866 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	0.22
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4937075; hg19: chr11-111997763;