rs8108392

Variant names:

• chr19-39293432-T-C
• rs8108392

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 0.151 in 152,018 control chromosomes in the GnomAD database, including 4,271 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 0.15 (4271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.150 AC: 22842 AN: 151900 Hom.: 4260 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.151 AC: 22895 AN: 152018 Hom.: 4271 Cov.: 31 AF XY: 0.145 AC XY: 10781 AN XY: 74336

African (AFR) AF: 0.446 AC: 18463 AN: 41352

American (AMR) AF: 0.0661 AC: 1009 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3470

East Asian (EAS) AF: 0.0347 AC: 180 AN: 5182

South Asian (SAS) AF: 0.0517 AC: 249 AN: 4818

European-Finnish (FIN) AF: 0.0253 AC: 269 AN: 10614

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0320 AC: 2175 AN: 68004

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.0688 Hom.: 1238

Bravo AF: 0.168

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.30
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs8108392; hg19: chr19-39784072;