chr6-32438565-A-C

Position:

• chr6-32438565-A-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 0.593 in 152,088 control chromosomes in the GnomAD database, including 27,309 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 0.59 (27309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90106 AN: 151970 Hom.: 27303 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.593 AC: 90140 AN: 152088 Hom.: 27309 Cov.: 32 AF XY: 0.596 AC XY: 44332 AN XY: 74342

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.604

Alfa AF: 0.653 Hom.: 52891

Bravo AF: 0.585

Asia WGS AF: 0.649 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.094
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129871; hg19: chr6-32406342;