rs1990670

Variant names:

• chr8-131695364-C-T
• rs1990670

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 0.0805 in 152,010 control chromosomes in the GnomAD database, including 519 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 0.080 (519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 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: 0.0805 AC: 12229 AN: 151892 Hom.: 519 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0738

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0805 AC: 12231 AN: 152010 Hom.: 519 Cov.: 32 AF XY: 0.0842 AC XY: 6256 AN XY: 74302

African (AFR) AF: 0.0616 AC: 2555 AN: 41494

American (AMR) AF: 0.0738 AC: 1126 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0829 AC: 287 AN: 3462

East Asian (EAS) AF: 0.0772 AC: 397 AN: 5140

South Asian (SAS) AF: 0.139 AC: 668 AN: 4812

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10570

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5406 AN: 67962

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0829 Hom.: 73

Bravo AF: 0.0730

Asia WGS AF: 0.0830 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1990670; hg19: chr8-132707611;