19-47579783-T-G

Variant names:

• chr19-47579783-T-G
• rs2341000

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 0.403 in 151,946 control chromosomes in the GnomAD database, including 15,191 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 (15191 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 61287 AN: 151828 Hom.: 15199 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.403 AC: 61271 AN: 151946 Hom.: 15191 Cov.: 31 AF XY: 0.406 AC XY: 30194 AN XY: 74278

African (AFR) AF: 0.102 AC: 4235 AN: 41486

American (AMR) AF: 0.409 AC: 6224 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1886 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2833 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2050 AN: 4812

European-Finnish (FIN) AF: 0.584 AC: 6166 AN: 10562

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36559 AN: 67920

Other (OTH) AF: 0.418 AC: 883 AN: 2110

Alfa AF: 0.499 Hom.: 42715

Bravo AF: 0.381

Asia WGS AF: 0.439 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2341000; hg19: chr19-48083040;