chr19-43675804-C-T

Variant names:

• chr19-43675804-C-T
• rs344772
• ENST00000830545.1:n.190-4679C>T

Variant summary

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

The ENST00000830545.1(ENSG00000308028):​n.190-4679C>T 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 150,604 control chromosomes in the GnomAD database, including 25,137 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 (25137 hom., cov: 28)
• Consequence: ENSG00000308028 ENST00000830545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 10 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 = 0.614 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.190-4679C>T		intron	N/A
	ENSG00000308028	ENST00000830546.1		n.166-1404C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 86696 AN: 150488 Hom.: 25110 Cov.: 28

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.576 AC: 86779 AN: 150604 Hom.: 25137 Cov.: 28 AF XY: 0.573 AC XY: 42055 AN XY: 73438

African (AFR) AF: 0.515 AC: 21088 AN: 40910

American (AMR) AF: 0.588 AC: 8872 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1940 AN: 3464

East Asian (EAS) AF: 0.469 AC: 2361 AN: 5034

South Asian (SAS) AF: 0.484 AC: 2295 AN: 4746

European-Finnish (FIN) AF: 0.625 AC: 6458 AN: 10334

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 41928 AN: 67742

Other (OTH) AF: 0.590 AC: 1237 AN: 2098

Alfa AF: 0.596 Hom.: 15510

Bravo AF: 0.569

Asia WGS AF: 0.484 AC: 1684 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	0.15
DANN	Benign	0.28
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs344772; hg19: chr19-44179956;