rs3130270

Variant names:

• chr6-33340444-A-G
• rs3130270

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.501 AC: 20665 AN: 41260

American (AMR) AF: 0.530 AC: 8069 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1877 AN: 5168

South Asian (SAS) AF: 0.625 AC: 3005 AN: 4806

European-Finnish (FIN) AF: 0.522 AC: 5406 AN: 10348

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34732 AN: 67824

Other (OTH) AF: 0.504 AC: 1059 AN: 2102

Alfa AF: 0.514 Hom.: 28201

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3130270; hg19: chr6-33308221;