rs9670198

Variant names:

• chr13-30770316-T-A
• rs9670198

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 0.0656 in 152,160 control chromosomes in the GnomAD database, including 459 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 0.066 (459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0655 AC: 9966 AN: 152042 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0656 AC: 9987 AN: 152160 Hom.: 459 Cov.: 32 AF XY: 0.0651 AC XY: 4843 AN XY: 74392

African (AFR) AF: 0.127 AC: 5268 AN: 41488

American (AMR) AF: 0.0328 AC: 502 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.151 AC: 778 AN: 5164

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4822

European-Finnish (FIN) AF: 0.0542 AC: 574 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0362 AC: 2460 AN: 68006

Other (OTH) AF: 0.0458 AC: 97 AN: 2116

Alfa AF: 0.0556 Hom.: 39

Bravo AF: 0.0669

Asia WGS AF: 0.0780 AC: 271 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9670198; hg19: chr13-31344453;