4-40044067-C-T

Variant names:

• chr4-40044067-C-T
• rs17585937
• ENST00000381811.2:n.463G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000381811.2(ENSG00000293349):​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: ENSG00000293349 ENST00000381811.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 7 publications found

Genes affected

ENSG00000293349 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000381811.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC344967	NR_027277.2		n.463G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293349	ENST00000381811.2	TSL:2	n.463G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000205794	ENST00000507914.2	TSL:6	n.69G>A		non_coding_transcript_exon	Exon 1 of 1

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

GnomAD2 exomes AF: 0.112 AC: 16009 AN: 143136 AF XY: 0.114

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 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

African (AFR) AF: 0.0621 AC: 958 AN: 15418

American (AMR) AF: 0.114 AC: 3828 AN: 33692

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 1548 AN: 18820

East Asian (EAS) AF: 0.105 AC: 3271 AN: 31140

South Asian (SAS) AF: 0.143 AC: 8860 AN: 61876

European-Finnish (FIN) AF: 0.115 AC: 4239 AN: 36952

Middle Eastern (MID) AF: 0.0964 AC: 371 AN: 3848

European-Non Finnish (NFE) AF: 0.105 AC: 31893 AN: 303494

Other (OTH) AF: 0.105 AC: 3020 AN: 28880

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

African (AFR) AF: 0.0641 AC: 2662 AN: 41546

American (AMR) AF: 0.0888 AC: 1358 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3468

East Asian (EAS) AF: 0.116 AC: 599 AN: 5170

South Asian (SAS) AF: 0.148 AC: 716 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1147 AN: 10578

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7006 AN: 68000

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.0978 Hom.: 1156

Bravo AF: 0.0896

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17585937; hg19: chr4-40045687;