rs2516486

Variant names:

• chr6-31526425-A-G
• rs2516486

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 0.127 in 152,170 control chromosomes in the GnomAD database, including 1,453 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 0.13 (1453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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: 0.127 AC: 19329 AN: 152052 Hom.: 1451 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.127 AC: 19350 AN: 152170 Hom.: 1453 Cov.: 32 AF XY: 0.135 AC XY: 10031 AN XY: 74390

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.129

Alfa AF: 0.113 Hom.: 122

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516486; hg19: chr6-31494202;