rs2517518

Positions:

• chr6-31060568-C-T

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 0.208 in 152,122 control chromosomes in the GnomAD database, including 3,641 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 0.21 (3641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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: 0.208 AC: 31567 AN: 152004 Hom.: 3633 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.208 AC: 31604 AN: 152122 Hom.: 3641 Cov.: 32 AF XY: 0.210 AC XY: 15651 AN XY: 74366

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.237

Alfa AF: 0.178 Hom.: 2919

Bravo AF: 0.213

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517518; hg19: chr6-31028345;