19-43690629-C-T

Variant names:

• chr19-43690629-C-T
• rs346043
• ENST00000636801.1:n.160+468C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_172891.1(LOC105372412):​n.826+498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,162 control chromosomes in the GnomAD database, including 50,054 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 0.80 (50054 hom., cov: 32)
• Consequence: LOC105372412 NR_172891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685

Genes affected

ENSG00000283525 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372412	NR_172891.1	n.826+498C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283525	ENST00000636801.1	n.160+468C>T		intron_variant	Intron 1 of 5	6

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122324 AN: 152044 Hom.: 50001 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.805 AC: 122432 AN: 152162 Hom.: 50054 Cov.: 32 AF XY: 0.801 AC XY: 59610 AN XY: 74380

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.802

Alfa AF: 0.785 Hom.: 11283

Bravo AF: 0.829

Asia WGS AF: 0.791 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.1
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346043; hg19: chr19-44194781;