rs3134775

chr6-31233580-A-Cchr6-31233580-A-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 0.268 in 152,142 control chromosomes in the GnomAD database, including 5,684 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 0.27 (5684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.268 AC: 40689 AN: 152024 Hom.: 5684 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.268 AC: 40702 AN: 152142 Hom.: 5684 Cov.: 32 AF XY: 0.265 AC XY: 19702 AN XY: 74356

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.279

Alfa AF: 0.164 Hom.: 333

Bravo AF: 0.264

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.9
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134775; hg19: chr6-31201357;