19-43677043-C-T

Variant names:

• chr19-43677043-C-T
• rs8113334
• ENST00000830545.1:n.190-3440C>T

Variant summary

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

The ENST00000830545.1(ENSG00000308028):​n.190-3440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,090 control chromosomes in the GnomAD database, including 50,028 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 0.81 (50028 hom., cov: 31)
• Consequence: ENSG00000308028 ENST00000830545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904724	XR_007067264.1	n.876-3440C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308028	ENST00000830545.1	n.190-3440C>T		intron_variant	Intron 1 of 1
ENSG00000308028	ENST00000830546.1	n.166-165C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122816 AN: 151972 Hom.: 49979 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.808 AC: 122927 AN: 152090 Hom.: 50028 Cov.: 31 AF XY: 0.804 AC XY: 59801 AN XY: 74340

African (AFR) AF: 0.869 AC: 36064 AN: 41504

American (AMR) AF: 0.746 AC: 11373 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2851 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2698 AN: 5168

South Asian (SAS) AF: 0.683 AC: 3292 AN: 4818

European-Finnish (FIN) AF: 0.837 AC: 8848 AN: 10574

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55144 AN: 67996

Other (OTH) AF: 0.813 AC: 1714 AN: 2108

Alfa AF: 0.817 Hom.: 10536

Bravo AF: 0.803

Asia WGS AF: 0.638 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs8113334; hg19: chr19-44181195;