8-19990179-C-A

Variant names:

• chr8-19990179-C-A
• rs10503669

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 0.085 in 152,124 control chromosomes in the GnomAD database, including 561 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 0.085 (561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 86 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12939 AN: 152006 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0850 AC: 12928 AN: 152124 Hom.: 561 Cov.: 32 AF XY: 0.0842 AC XY: 6259 AN XY: 74352

African (AFR) AF: 0.0599 AC: 2485 AN: 41500

American (AMR) AF: 0.0740 AC: 1131 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0995 AC: 345 AN: 3468

East Asian (EAS) AF: 0.109 AC: 561 AN: 5168

South Asian (SAS) AF: 0.0947 AC: 456 AN: 4814

European-Finnish (FIN) AF: 0.0881 AC: 932 AN: 10576

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0981 AC: 6674 AN: 68006

Other (OTH) AF: 0.0834 AC: 175 AN: 2098

Alfa AF: 0.0918 Hom.: 2432

Bravo AF: 0.0818

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10503669; hg19: chr8-19847690;