6-32474484-T-C

Variant names:

• chr6-32474484-T-C
• rs6901541

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 0.295 in 114,408 control chromosomes in the GnomAD database, including 3,766 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 0.29 (3766 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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: 0.295 AC: 33693 AN: 114312 Hom.: 3766 Cov.: 29

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.295 AC: 33714 AN: 114408 Hom.: 3766 Cov.: 29 AF XY: 0.295 AC XY: 16523 AN XY: 55934

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.292

Alfa AF: 0.284 Hom.: 1582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6901541; hg19: chr6-32442261;