6-32240547-C-T

Position:

• chr6-32240547-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 0.302 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;