rs17212090

Variant names:

• chr6-32683032-C-T
• rs17212090

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 0.258 in 151,846 control chromosomes in the GnomAD database, including 5,369 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 0.26 (5369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 17 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 = 0.426 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: 0.258 AC: 39198 AN: 151728 Hom.: 5375 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.258 AC: 39209 AN: 151846 Hom.: 5369 Cov.: 32 AF XY: 0.255 AC XY: 18889 AN XY: 74216

African (AFR) AF: 0.261 AC: 10819 AN: 41396

American (AMR) AF: 0.240 AC: 3659 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3472

East Asian (EAS) AF: 0.441 AC: 2268 AN: 5146

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4806

European-Finnish (FIN) AF: 0.182 AC: 1928 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17378 AN: 67904

Other (OTH) AF: 0.276 AC: 582 AN: 2106

Alfa AF: 0.257 Hom.: 9225

Bravo AF: 0.263

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17212090; hg19: chr6-32650809;