chr19-40954716-G-A

Variant names:

• chr19-40954716-G-A
• rs8109818

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 0.376 in 151,980 control chromosomes in the GnomAD database, including 12,346 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 0.38 (12346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.376 AC: 57139 AN: 151864 Hom.: 12324 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.376 AC: 57201 AN: 151980 Hom.: 12346 Cov.: 32 AF XY: 0.377 AC XY: 27970 AN XY: 74254

African (AFR) AF: 0.589 AC: 24409 AN: 41414

American (AMR) AF: 0.405 AC: 6176 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1308 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2038 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2445 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18306 AN: 67992

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.308 Hom.: 31615

Bravo AF: 0.394

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs8109818; hg19: chr19-41460621;