rs17212420

Variant names:

• chr6-32684623-C-T
• rs17212420

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 0.256 in 151,312 control chromosomes in the GnomAD database, including 5,301 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 (5301 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.256 AC: 38738 AN: 151196 Hom.: 5308 Cov.: 30

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.256 AC: 38747 AN: 151312 Hom.: 5301 Cov.: 30 AF XY: 0.252 AC XY: 18660 AN XY: 73934

African (AFR) AF: 0.259 AC: 10696 AN: 41258

American (AMR) AF: 0.238 AC: 3606 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1002 AN: 3452

East Asian (EAS) AF: 0.431 AC: 2203 AN: 5106

South Asian (SAS) AF: 0.241 AC: 1153 AN: 4790

European-Finnish (FIN) AF: 0.178 AC: 1871 AN: 10488

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17247 AN: 67740

Other (OTH) AF: 0.272 AC: 572 AN: 2104

Alfa AF: 0.256 Hom.: 2811

Asia WGS AF: 0.375 AC: 1294 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs17212420; hg19: chr6-32652400; COSMIC: COSV64604088;