19-41854001-C-T

Variant names:

• chr19-41854001-C-T
• rs6509002

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 0.399 in 151,916 control chromosomes in the GnomAD database, including 13,866 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 (13866 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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: 0.399 AC: 60545 AN: 151798 Hom.: 13865 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.399 AC: 60556 AN: 151916 Hom.: 13866 Cov.: 31 AF XY: 0.400 AC XY: 29659 AN XY: 74234

African (AFR) AF: 0.153 AC: 6344 AN: 41438

American (AMR) AF: 0.474 AC: 7235 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2204 AN: 5144

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4818

European-Finnish (FIN) AF: 0.449 AC: 4738 AN: 10552

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34064 AN: 67922

Other (OTH) AF: 0.434 AC: 914 AN: 2108

Alfa AF: 0.461 Hom.: 11605

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6509002;

hg19: chr19-42358069;