rs17212420

chr6-32684623-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.272

Alfa AF: 0.259 Hom.: 1524

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

Splicing

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

Publications

LitVar

Other links and lift over

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