19-23439705-G-A

Variant names:

• chr19-23439705-G-A
• rs629359
• ENST00000817021.1:n.392G>A

Variant summary

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

The ENST00000817021.1(ENSG00000306337):​n.392G>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 0.338 in 151,918 control chromosomes in the GnomAD database, including 9,904 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 0.34 (9904 hom., cov: 32)
• Consequence: ENSG00000306337 ENST00000817021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

ENSG00000306337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817021.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306337	ENST00000817021.1		n.392G>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51262 AN: 151800 Hom.: 9869 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.306

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.338 AC: 51342 AN: 151918 Hom.: 9904 Cov.: 32 AF XY: 0.334 AC XY: 24764 AN XY: 74236

African (AFR) AF: 0.538 AC: 22282 AN: 41418

American (AMR) AF: 0.205 AC: 3135 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2031 AN: 5132

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4808

European-Finnish (FIN) AF: 0.246 AC: 2593 AN: 10554

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 18002 AN: 67956

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.311 Hom.: 1081

Bravo AF: 0.345

Asia WGS AF: 0.345 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.31
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs629359; hg19: chr19-23622507;