6-32421528-T-C

Variant names:

• chr6-32421528-T-C
• rs9268557

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 0.462 in 152,114 control chromosomes in the GnomAD database, including 16,800 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 0.46 (16800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

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 = 0.544 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: 0.462 AC: 70262 AN: 151996 Hom.: 16788 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.462 AC: 70307 AN: 152114 Hom.: 16800 Cov.: 33 AF XY: 0.469 AC XY: 34890 AN XY: 74374

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.469

Alfa AF: 0.489 Hom.: 14891

Bravo AF: 0.457

Asia WGS AF: 0.501 AC: 1741 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	5.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268557; hg19: chr6-32389305;