rs2107506

Variant names:

• chr5-135964588-C-G
• rs2107506

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.551 AC: 22861 AN: 41478

American (AMR) AF: 0.527 AC: 8040 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2742 AN: 5164

South Asian (SAS) AF: 0.499 AC: 2406 AN: 4820

European-Finnish (FIN) AF: 0.440 AC: 4627 AN: 10524

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30950 AN: 67946

Other (OTH) AF: 0.484 AC: 1023 AN: 2112

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2107506; hg19: chr5-135300277;