chr6-32411712-C-T

Position:

• chr6-32411712-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 0.24 in 152,170 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32411712C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36454 AN: 152052 Hom.: 4591 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.240 AC: 36467 AN: 152170 Hom.: 4590 Cov.: 33 AF XY: 0.236 AC XY: 17531 AN XY: 74392

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.232

Alfa AF: 0.268 Hom.: 3125

Bravo AF: 0.253

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268516; hg19: chr6-32379489;