chr19-17288816-T-C

Variant names:

• chr19-17288816-T-C
• rs11668840

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 0.473 in 151,498 control chromosomes in the GnomAD database, including 17,362 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 0.47 (17362 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.473 AC: 71653 AN: 151378 Hom.: 17344 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.473 AC: 71722 AN: 151498 Hom.: 17362 Cov.: 31 AF XY: 0.474 AC XY: 35052 AN XY: 73996

African (AFR) AF: 0.413 AC: 16975 AN: 41086

American (AMR) AF: 0.425 AC: 6480 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1765 AN: 3464

East Asian (EAS) AF: 0.318 AC: 1632 AN: 5130

South Asian (SAS) AF: 0.477 AC: 2294 AN: 4806

European-Finnish (FIN) AF: 0.569 AC: 6008 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34976 AN: 67910

Other (OTH) AF: 0.475 AC: 999 AN: 2104

Alfa AF: 0.505 Hom.: 8928

Bravo AF: 0.459

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs11668840; hg19: chr19-17399625;