rs3130270

chr6-33340444-A-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 0.51 in 151,404 control chromosomes in the GnomAD database, including 19,866 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 0.51 (19866 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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: 0.510 AC: 77130 AN: 151290 Hom.: 19845 Cov.: 30

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.510 AC: 77200 AN: 151404 Hom.: 19866 Cov.: 30 AF XY: 0.513 AC XY: 37947 AN XY: 73972

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.504

Alfa AF: 0.514 Hom.: 12683

Bravo AF: 0.506

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	7.0
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130270; hg19: chr6-33308221;