rs2953308

Positions:

• chr11-40108459-A-G

Variant summary

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

The ENST00000624239.1(ENSG00000279675):​n.4141T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,884 control chromosomes in the GnomAD database, including 17,845 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 0.47 (17845 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279675 ENST00000624239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

ENSG00000279675 (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 = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40108459A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279675	ENST00000624239.1	n.4141T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70841 AN: 151766 Hom.: 17791 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.483

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.467 AC: 70960 AN: 151884 Hom.: 17845 Cov.: 32 AF XY: 0.461 AC XY: 34238 AN XY: 74232

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.486

Alfa AF: 0.426 Hom.: 3790

Bravo AF: 0.494

Asia WGS AF: 0.463 AC: 1607 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2953308; hg19: chr11-40130009;