19-56874568-T-C

Variant names:

• chr19-56874568-T-C
• rs10420985

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 0.928 in 152,156 control chromosomes in the GnomAD database, including 65,678 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 0.93 (65678 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141139 AN: 152038 Hom.: 65619 Cov.: 30

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.928 AC: 141257 AN: 152156 Hom.: 65678 Cov.: 30 AF XY: 0.930 AC XY: 69167 AN XY: 74380

African (AFR) AF: 0.976 AC: 40517 AN: 41514

American (AMR) AF: 0.925 AC: 14139 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5150 AN: 5156

South Asian (SAS) AF: 0.964 AC: 4635 AN: 4810

European-Finnish (FIN) AF: 0.931 AC: 9865 AN: 10600

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60994 AN: 68012

Other (OTH) AF: 0.907 AC: 1910 AN: 2106

Alfa AF: 0.915 Hom.: 7416

Bravo AF: 0.928

Asia WGS AF: 0.982 AC: 3415 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	2.8
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10420985; hg19: chr19-57385936;