6-32774091-T-C

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 0.259 in 152,072 control chromosomes in the GnomAD database, including 5,459 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 0.26 (5459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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: 0.259 AC: 39313 AN: 151954 Hom.: 5450 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.259 AC: 39358 AN: 152072 Hom.: 5459 Cov.: 32 AF XY: 0.266 AC XY: 19781 AN XY: 74308

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.249

Alfa AF: 0.274 Hom.: 7864

Bravo AF: 0.253

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621416; hg19: chr6-32741868;