11-40108459-A-G

Position:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279675	ENST00000624239.1	n.4141T>C		non_coding_transcript_exon_variant	Exon 1 of 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;