rs8109818

chr19-40954716-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;