rs10414043

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.102

Alfa AF: 0.123 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10414043; hg19: chr19-45415713;