rs3135353

Positions:

• chr6-32425100-C-T

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 0.0923 in 152,236 control chromosomes in the GnomAD database, including 936 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 0.092 (936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.0924 AC: 14055 AN: 152118 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0923 AC: 14049 AN: 152236 Hom.: 936 Cov.: 32 AF XY: 0.0882 AC XY: 6564 AN XY: 74432

Gnomad4 AFR AF: 0.0230

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.127 Hom.: 1295

Bravo AF: 0.0867

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135353; hg19: chr6-32392877;