19-43673715-T-C

Variant names:

• chr19-43673715-T-C
• rs344780
• ENST00000830545.1:n.189+3235T>C

Variant summary

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

The ENST00000830545.1(ENSG00000308028):​n.189+3235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 147,114 control chromosomes in the GnomAD database, including 46,537 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 0.79 (46537 hom., cov: 23)
• Consequence: ENSG00000308028 ENST00000830545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 5 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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+3235T>C		intron	N/A
	ENSG00000308028	ENST00000830546.1		n.165+3235T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.794 AC: 116659 AN: 147018 Hom.: 46496 Cov.: 23

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.794 AC: 116752 AN: 147114 Hom.: 46537 Cov.: 23 AF XY: 0.787 AC XY: 56182 AN XY: 71344

African (AFR) AF: 0.898 AC: 35771 AN: 39820

American (AMR) AF: 0.758 AC: 11084 AN: 14626

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2743 AN: 3454

East Asian (EAS) AF: 0.555 AC: 2743 AN: 4938

South Asian (SAS) AF: 0.671 AC: 3116 AN: 4642

European-Finnish (FIN) AF: 0.738 AC: 6881 AN: 9318

Middle Eastern (MID) AF: 0.830 AC: 239 AN: 288

European-Non Finnish (NFE) AF: 0.773 AC: 51884 AN: 67102

Other (OTH) AF: 0.797 AC: 1628 AN: 2042

Alfa AF: 0.701 Hom.: 1907

Bravo AF: 0.794

Asia WGS AF: 0.632 AC: 2174 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.17
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs344780; hg19: chr19-44177867;