rs8190870

Positions:

• chr8-18223763-C-T

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 0.163 in 152,228 control chromosomes in the GnomAD database, including 2,267 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 0.16 (2253 hom., cov: 31)
  • Exomes 𝑓: 0.17 (14 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24590 AN: 151362 Hom.: 2246 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.169 AC: 126 AN: 744 Hom.: 14 AF XY: 0.184 AC XY: 79 AN XY: 430

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.163 AC: 24625 AN: 151484 Hom.: 2253 Cov.: 31 AF XY: 0.162 AC XY: 11965 AN XY: 74008

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.139

Alfa AF: 0.148 Hom.: 1645

Bravo AF: 0.158

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8190870; hg19: chr8-18081272;