ENST00000830545.1:n.189+339G>T

Variant names:

• chr19-43670819-G-T
• rs2356338
• ENST00000830545.1:n.189+339G>T

Variant summary

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

The ENST00000830545.1(ENSG00000308028):​n.189+339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,752 control chromosomes in the GnomAD database, including 4,622 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 0.22 (4622 hom., cov: 29)
• Consequence: ENSG00000308028 ENST00000830545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 7 publications found

Genes affected

ENSG00000308028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830545.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308028	ENST00000830545.1		n.189+339G>T		intron	N/A
	ENSG00000308028	ENST00000830546.1		n.165+339G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33996 AN: 151636 Hom.: 4620 Cov.: 29

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.224 AC: 34005 AN: 151752 Hom.: 4622 Cov.: 29 AF XY: 0.226 AC XY: 16790 AN XY: 74134

African (AFR) AF: 0.0805 AC: 3332 AN: 41378

American (AMR) AF: 0.179 AC: 2733 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3468

East Asian (EAS) AF: 0.0986 AC: 509 AN: 5164

South Asian (SAS) AF: 0.252 AC: 1213 AN: 4812

European-Finnish (FIN) AF: 0.371 AC: 3902 AN: 10512

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20654 AN: 67870

Other (OTH) AF: 0.222 AC: 469 AN: 2110

Alfa AF: 0.173 Hom.: 419

Bravo AF: 0.200

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.83
PhyloP100		-2.0
PromoterAI		0.0094	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2356338; hg19: chr19-44174971;