rs2516400

Positions:

• chr6-31513328-G-A

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 0.316 in 151,946 control chromosomes in the GnomAD database, including 7,843 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 0.32 (7843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48039 AN: 151828 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.316 AC: 48081 AN: 151946 Hom.: 7843 Cov.: 32 AF XY: 0.312 AC XY: 23181 AN XY: 74272

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.300

Alfa AF: 0.312 Hom.: 4236

Bravo AF: 0.315

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516400; hg19: chr6-31481105;