rs17835853

chr5-51877490-G-Achr5-51877490-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0296 in 152,154 control chromosomes in the GnomAD database, including 108 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 0.030 (108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0296 (4506/152154) while in subpopulation AFR AF= 0.0487 (2022/41494). AF 95% confidence interval is 0.047. There are 108 homozygotes in gnomad4. There are 2060 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 108 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0296 AC: 4499 AN: 152036 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00633

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0296 AC: 4506 AN: 152154 Hom.: 108 Cov.: 32 AF XY: 0.0277 AC XY: 2060 AN XY: 74388

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00415

Gnomad4 FIN AF: 0.00633

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.00978 Hom.: 1

Bravo AF: 0.0314

Asia WGS AF: 0.00520 AC: 18 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17835853; hg19: chr5-51173324;