rs3135365

Positions:

• chr6-32421478-C-A
• chr6-32421478-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;