rs2734842

Positions:

• chr11-113409552-G-C

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.245-1995G>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 0.541 in 152,302 control chromosomes in the GnomAD database, including 25,597 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 0.54 (25556 hom., cov: 33)
  • Exomes 𝑓: 0.65 (41 hom.)
• Consequence: ENST00000546284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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.245-1995G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82243 AN: 151996 Hom.: 25554 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.649 AC: 122 AN: 188 Hom.: 41 AF XY: 0.710 AC XY: 88 AN XY: 124

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.779

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.541 AC: 82254 AN: 152114 Hom.: 25556 Cov.: 33 AF XY: 0.541 AC XY: 40217 AN XY: 74346

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.595

Alfa AF: 0.617 Hom.: 3901

Bravo AF: 0.527

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734842; hg19: chr11-113280274;