chr4-40044067-C-T

Position:

• chr4-40044067-C-T

Variant summary

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

The ENST00000381811.2(ENSG00000205794):​n.463G>A 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 0.105 in 686,308 control chromosomes in the GnomAD database, including 4,115 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 0.092 (685 hom., cov: 32)
  • Exomes 𝑓: 0.11 (3430 hom.)
• Consequence: ENSG00000205794 ENST00000381811.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564

Genes affected

ENSG00000205794 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC344967	NR_027277.2	n.463G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000205794	ENST00000381811.2	n.463G>A		non_coding_transcript_exon_variant	3/3	2
ENSG00000205794	ENST00000507914.2	n.69G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14045 AN: 152070 Hom.: 687 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0963

GnomAD3 exomes AF: 0.112 AC: 16009 AN: 143136 Hom.: 983 AF XY: 0.114 AC XY: 8665 AN XY: 75906

Gnomad AFR exome AF: 0.0615

Gnomad AMR exome AF: 0.114

Gnomad ASJ exome AF: 0.0818

Gnomad EAS exome AF: 0.123

Gnomad SAS exome AF: 0.149

Gnomad FIN exome AF: 0.119

Gnomad NFE exome AF: 0.105

Gnomad OTH exome AF: 0.114

GnomAD4 exome AF: 0.109 AC: 57988 AN: 534120 Hom.: 3430 Cov.: 4 AF XY: 0.111 AC XY: 32011 AN XY: 288250

Gnomad4 AFR exome AF: 0.0621

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.0823

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.143

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.105

GnomAD4 genome AF: 0.0923 AC: 14052 AN: 152188 Hom.: 685 Cov.: 32 AF XY: 0.0920 AC XY: 6844 AN XY: 74410

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.0966 Hom.: 886

Bravo AF: 0.0896

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17585937; hg19: chr4-40045687;