19-40984499-G-C

Variant names:

• chr19-40984499-G-C
• rs10418990

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 0.698 in 151,838 control chromosomes in the GnomAD database, including 38,476 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 0.70 (38476 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105812 AN: 151720 Hom.: 38426 Cov.: 29

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.698 AC: 105921 AN: 151838 Hom.: 38476 Cov.: 29 AF XY: 0.700 AC XY: 51875 AN XY: 74158

African (AFR) AF: 0.901 AC: 37267 AN: 41384

American (AMR) AF: 0.759 AC: 11572 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2123 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3385 AN: 5156

South Asian (SAS) AF: 0.753 AC: 3604 AN: 4786

European-Finnish (FIN) AF: 0.586 AC: 6169 AN: 10530

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39740 AN: 67948

Other (OTH) AF: 0.688 AC: 1447 AN: 2104

Alfa AF: 0.518 Hom.: 1537

Bravo AF: 0.717

Asia WGS AF: 0.715 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.40
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10418990; hg19: chr19-41490404;