rs3016013

Variant names:

• chr6-31383465-G-A
• rs3016013

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 0.707 in 152,088 control chromosomes in the GnomAD database, including 38,261 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 0.71 (38261 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

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 (AMR) allele frequency at 95% confidence interval = 0.761 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: 0.707 AC: 107455 AN: 151970 Hom.: 38223 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.707 AC: 107546 AN: 152088 Hom.: 38261 Cov.: 32 AF XY: 0.706 AC XY: 52463 AN XY: 74350

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.734

Alfa AF: 0.717 Hom.: 7470

Bravo AF: 0.708

Asia WGS AF: 0.677 AC: 2357 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	2.6
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3016013; hg19: chr6-31351242;