chr6-32421478-C-A

Variant names:

• chr6-32421478-C-A
• rs3135365

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 0.796 in 152,108 control chromosomes in the GnomAD database, including 48,308 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 0.80 (48308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.796 AC: 120976 AN: 151990 Hom.: 48277 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.796 AC: 121058 AN: 152108 Hom.: 48308 Cov.: 32 AF XY: 0.799 AC XY: 59418 AN XY: 74360

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.815

Alfa AF: 0.805 Hom.: 34403

Bravo AF: 0.793

Asia WGS AF: 0.802 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.8
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: rs3135365; hg19: chr6-32389255;