6-30225736-A-G

Variant names:

• chr6-30225736-A-G
• rs3132666

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 0.421 in 152,092 control chromosomes in the GnomAD database, including 13,668 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 0.42 (13668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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: 0.421 AC: 64026 AN: 151972 Hom.: 13641 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.421 AC: 64106 AN: 152092 Hom.: 13668 Cov.: 32 AF XY: 0.418 AC XY: 31064 AN XY: 74342

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.389

Alfa AF: 0.434 Hom.: 4267

Bravo AF: 0.420

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132666; hg19: chr6-30193513;