rs2107506

Variant names:

• chr5-135964588-C-G
• rs2107506

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 0.493 in 151,970 control chromosomes in the GnomAD database, including 18,606 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 0.49 (18606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.493 AC: 74834 AN: 151850 Hom.: 18585 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.493 AC: 74913 AN: 151970 Hom.: 18606 Cov.: 33 AF XY: 0.492 AC XY: 36524 AN XY: 74258

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.484

Alfa AF: 0.475 Hom.: 2139

Bravo AF: 0.505

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2107506; hg19: chr5-135300277;