ENST00000623895.1:n.3082G>A

Variant names:

• chr19-44912456-G-A
• rs10414043
• ENST00000623895.1:n.3082G>A

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3082G>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 0.134 in 152,240 control chromosomes in the GnomAD database, including 1,479 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 0.13 (1479 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 56 publications found

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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
ENSG00000280087	ENST00000623895.1	n.3082G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20281 AN: 152012 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0978

GnomAD4 exome AF: 0.100 AC: 11 AN: 110 Hom.: 0 Cov.: 0 AF XY: 0.0921 AC XY: 7 AN XY: 76

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.120 AC: 11 AN: 92

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.134 AC: 20323 AN: 152130 Hom.: 1479 Cov.: 32 AF XY: 0.136 AC XY: 10114 AN XY: 74356

African (AFR) AF: 0.189 AC: 7844 AN: 41484

American (AMR) AF: 0.0939 AC: 1436 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.0967 AC: 500 AN: 5170

South Asian (SAS) AF: 0.0769 AC: 371 AN: 4824

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10578

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7659 AN: 68006

Other (OTH) AF: 0.102 AC: 215 AN: 2108

Alfa AF: 0.0721 Hom.: 144

Bravo AF: 0.130

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.62
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs10414043; hg19: chr19-45415713;