rs2197089

chr8-19968862-G-A

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 0.606 in 152,008 control chromosomes in the GnomAD database, including 29,183 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 0.61 (29183 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91989 AN: 151890 Hom.: 29141 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.606 AC: 92075 AN: 152008 Hom.: 29183 Cov.: 31 AF XY: 0.599 AC XY: 44494 AN XY: 74290

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.570

Alfa AF: 0.559 Hom.: 45795

Bravo AF: 0.610

Asia WGS AF: 0.392 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.16
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2197089; hg19: chr8-19826373;