chr11-113408708-G-A

Position:

• chr11-113408708-G-A

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.244+2741G>A 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 0.571 in 151,916 control chromosomes in the GnomAD database, including 26,799 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 0.57 (26799 hom., cov: 31)
• Consequence: ENST00000546284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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
	ENST00000546284.1	n.244+2741G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86699 AN: 151798 Hom.: 26799 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.571 AC: 86717 AN: 151916 Hom.: 26799 Cov.: 31 AF XY: 0.569 AC XY: 42270 AN XY: 74234

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.616

Alfa AF: 0.682 Hom.: 47168

Bravo AF: 0.560

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2242592; hg19: chr11-113279430;