chr6-32240547-C-T

Variant names:

• chr6-32240547-C-T
• rs424232

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 0.302 in 151,978 control chromosomes in the GnomAD database, including 7,286 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 0.30 (7286 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

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 (SAS) allele frequency at 95% confidence interval = 0.366 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: 0.302 AC: 45911 AN: 151860 Hom.: 7284 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.302 AC: 45931 AN: 151978 Hom.: 7286 Cov.: 31 AF XY: 0.297 AC XY: 22083 AN XY: 74282

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.346

Alfa AF: 0.314 Hom.: 10509

Bravo AF: 0.309

Asia WGS AF: 0.346 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs424232; hg19: chr6-32208324;