chr6-32420032-T-C

Position:

• chr6-32420032-T-C

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 0.173 in 151,950 control chromosomes in the GnomAD database, including 2,484 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 (2484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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: 0.173 AC: 26322 AN: 151830 Hom.: 2487 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.173 AC: 26318 AN: 151950 Hom.: 2484 Cov.: 31 AF XY: 0.173 AC XY: 12833 AN XY: 74278

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.163

Alfa AF: 0.201 Hom.: 4702

Bravo AF: 0.178

Asia WGS AF: 0.133 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395163; hg19: chr6-32387809;