rs3130299

Variant names:

• chr6-32235760-A-G
• rs3130299

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 0.246 in 151,944 control chromosomes in the GnomAD database, including 4,994 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 0.25 (4994 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 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: 0.246 AC: 37322 AN: 151826 Hom.: 4993 Cov.: 30

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.246 AC: 37353 AN: 151944 Hom.: 4994 Cov.: 30 AF XY: 0.244 AC XY: 18137 AN XY: 74282

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.281

Alfa AF: 0.263 Hom.: 7487

Bravo AF: 0.255

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130299; hg19: chr6-32203537;