chr19-43673836-T-G

Variant names:

• chr19-43673836-T-G
• rs344779
• ENST00000830545.1:n.189+3356T>G

Variant summary

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

The ENST00000830545.1(ENSG00000308028):​n.189+3356T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,940 control chromosomes in the GnomAD database, including 25,387 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 0.58 (25387 hom., cov: 32)
• Consequence: ENSG00000308028 ENST00000830545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 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+3356T>G		intron	N/A
	ENSG00000308028	ENST00000830546.1		n.165+3356T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87395 AN: 151822 Hom.: 25363 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.576 AC: 87474 AN: 151940 Hom.: 25387 Cov.: 32 AF XY: 0.572 AC XY: 42484 AN XY: 74246

African (AFR) AF: 0.513 AC: 21278 AN: 41450

American (AMR) AF: 0.590 AC: 8995 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2403 AN: 5176

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4812

European-Finnish (FIN) AF: 0.621 AC: 6546 AN: 10540

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42094 AN: 67942

Other (OTH) AF: 0.590 AC: 1241 AN: 2102

Alfa AF: 0.602 Hom.: 18463

Bravo AF: 0.569

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.79
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs344779; hg19: chr19-44177988;