rs3130299

Positions:

• chr6-32235760-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 0.246 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.32235760A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;