11-114320294-A-G

Position:

• chr11-114320294-A-G

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, non coding transcript 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: ENST00000544925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000544925.1	n.50+36228T>C		intron_variant, non_coding_transcript_variant		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;