rs8109818

Variant names:

• chr19-40954716-G-A
• rs8109818

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.400

Alfa AF: 0.299 Hom.: 13411

Bravo AF: 0.394

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8109818; hg19: chr19-41460621;