19-348743-T-C

Variant names:

• chr19-348743-T-C
• rs6510725

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 0.518 in 151,916 control chromosomes in the GnomAD database, including 21,082 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 0.52 (21082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78712 AN: 151798 Hom.: 21087 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.518 AC: 78730 AN: 151916 Hom.: 21082 Cov.: 32 AF XY: 0.520 AC XY: 38589 AN XY: 74224

African (AFR) AF: 0.389 AC: 16096 AN: 41414

American (AMR) AF: 0.533 AC: 8148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1841 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3535 AN: 5142

South Asian (SAS) AF: 0.690 AC: 3320 AN: 4814

European-Finnish (FIN) AF: 0.513 AC: 5408 AN: 10538

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38655 AN: 67952

Other (OTH) AF: 0.514 AC: 1080 AN: 2102

Alfa AF: 0.524 Hom.: 20939

Bravo AF: 0.514

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6510725; hg19: chr19-348743;