rs12198798

Variant names:

• chr6-12509895-T-C
• rs12198798

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 0.171 in 151,938 control chromosomes in the GnomAD database, including 2,275 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 0.17 (2275 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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: 0.171 AC: 25936 AN: 151820 Hom.: 2271 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.171 AC: 25966 AN: 151938 Hom.: 2275 Cov.: 31 AF XY: 0.168 AC XY: 12482 AN XY: 74286

African (AFR) AF: 0.214 AC: 8865 AN: 41394

American (AMR) AF: 0.147 AC: 2242 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.184 AC: 954 AN: 5172

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10552

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10474 AN: 67952

Other (OTH) AF: 0.164 AC: 345 AN: 2106

Alfa AF: 0.172 Hom.: 1261

Bravo AF: 0.176

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12198798; hg19: chr6-12510127;