19-55372511-C-T

Variant names:

• chr19-55372511-C-T
• rs6509940

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 0.527 in 151,896 control chromosomes in the GnomAD database, including 21,234 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 0.53 (21234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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: 0.527 AC: 80002 AN: 151776 Hom.: 21227 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.527 AC: 80042 AN: 151896 Hom.: 21234 Cov.: 32 AF XY: 0.526 AC XY: 39071 AN XY: 74222

African (AFR) AF: 0.519 AC: 21508 AN: 41428

American (AMR) AF: 0.582 AC: 8893 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1833 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3550 AN: 5144

South Asian (SAS) AF: 0.544 AC: 2615 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5214 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34531 AN: 67900

Other (OTH) AF: 0.531 AC: 1116 AN: 2102

Alfa AF: 0.519 Hom.: 79480

Bravo AF: 0.536

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.46
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6509940; hg19: chr19-55883879;