11-114320294-A-G

Variant names:

• chr11-114320294-A-G
• rs2847476
• ENST00000544925.1:n.50+36228T>C

Variant summary

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

The ENST00000544925.1(ENSG00000256947):​n.50+36228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,040 control chromosomes in the GnomAD database, including 32,619 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 0.65 (32619 hom., cov: 32)
• Consequence: ENSG00000256947 ENST00000544925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986

Genes affected

ENSG00000256947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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
ENSG00000256947	ENST00000544925.1	n.50+36228T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98917 AN: 151922 Hom.: 32589 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.651 AC: 99000 AN: 152040 Hom.: 32619 Cov.: 32 AF XY: 0.653 AC XY: 48503 AN XY: 74304

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.626

Alfa AF: 0.603 Hom.: 58670

Bravo AF: 0.651

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2847476; hg19: chr11-114191016;