rs2169520

Variant names:

• chr5-63302626-T-C
• rs2169520

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 0.245 in 152,086 control chromosomes in the GnomAD database, including 5,260 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 0.24 (5260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

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 (AFR) allele frequency at 95% confidence interval = 0.382 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: 0.245 AC: 37157 AN: 151968 Hom.: 5250 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.245 AC: 37190 AN: 152086 Hom.: 5260 Cov.: 32 AF XY: 0.236 AC XY: 17542 AN XY: 74352

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.264

Alfa AF: 0.217 Hom.: 5049

Bravo AF: 0.264

Asia WGS AF: 0.130 AC: 455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169520; hg19: chr5-62598453;