6-32409105-T-G

Variant names:

• chr6-32409105-T-G
• rs9268501

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 0.555 in 152,084 control chromosomes in the GnomAD database, including 23,760 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 0.55 (23760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.555 AC: 84309 AN: 151966 Hom.: 23746 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.555 AC: 84363 AN: 152084 Hom.: 23760 Cov.: 32 AF XY: 0.559 AC XY: 41572 AN XY: 74342

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.566

Alfa AF: 0.489 Hom.: 4508

Bravo AF: 0.563

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268501; hg19: chr6-32376882;