chr6-32411712-C-T

Variant names:

• chr6-32411712-C-T
• rs9268516

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;