chr19-40986013-A-G

Variant names:

• chr19-40986013-A-G
• rs8109525

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 0.297 in 152,000 control chromosomes in the GnomAD database, including 7,458 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 0.30 (7458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 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: 0.297 AC: 45179 AN: 151882 Hom.: 7458 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.297 AC: 45203 AN: 152000 Hom.: 7458 Cov.: 32 AF XY: 0.302 AC XY: 22424 AN XY: 74308

African (AFR) AF: 0.161 AC: 6659 AN: 41434

American (AMR) AF: 0.361 AC: 5507 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2272 AN: 5162

South Asian (SAS) AF: 0.348 AC: 1679 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22791 AN: 67982

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.309 Hom.: 1024

Bravo AF: 0.291

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.35
DANN	Benign	0.85
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs8109525; hg19: chr19-41491918;