19-11843747-T-C

Variant names:

• chr19-11843747-T-C
• rs286246

Variant summary

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

The variant allele was found at a frequency of 0.404 in 151,960 control chromosomes in the GnomAD database, including 12,801 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 0.40 (12801 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 8 publications found

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 = 0.482 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61330 AN: 151844 Hom.: 12787 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.404 AC: 61380 AN: 151960 Hom.: 12801 Cov.: 31 AF XY: 0.396 AC XY: 29424 AN XY: 74288

African (AFR) AF: 0.487 AC: 20189 AN: 41428

American (AMR) AF: 0.350 AC: 5337 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3472

East Asian (EAS) AF: 0.152 AC: 784 AN: 5156

South Asian (SAS) AF: 0.264 AC: 1270 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3501 AN: 10564

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27719 AN: 67970

Other (OTH) AF: 0.392 AC: 823 AN: 2098

Alfa AF: 0.403 Hom.: 20991

Bravo AF: 0.412

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.95
DANN	Benign	0.29
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs286246; hg19: chr19-11954562;