chr19-43673715-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904724	XR_007067264.1	n.875+3235T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308028	ENST00000830545.1	n.189+3235T>C		intron_variant	Intron 1 of 1
ENSG00000308028	ENST00000830546.1	n.165+3235T>C		intron_variant	Intron 1 of 1

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 v4.3

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;