rs3020310

Variant names:

• chr6-151649219-A-G
• rs3020310

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 0.201 in 151,934 control chromosomes in the GnomAD database, including 3,190 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 0.20 (3190 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

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 = 0.245 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: 0.201 AC: 30468 AN: 151816 Hom.: 3186 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.201 AC: 30491 AN: 151934 Hom.: 3190 Cov.: 30 AF XY: 0.197 AC XY: 14663 AN XY: 74256

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.205

Alfa AF: 0.213 Hom.: 1386

Bravo AF: 0.201

Asia WGS AF: 0.163 AC: 568 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	1.2
DANN	Benign	0.089

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3020310; hg19: chr6-151970354;