rs25812

Positions:

• chr5-103037888-T-C

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 0.0197 in 152,306 control chromosomes in the GnomAD database, including 46 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 0.020 (46 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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 = 0.0574 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: 0.0196 AC: 2988 AN: 152188 Hom.: 46 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0197 AC: 2993 AN: 152306 Hom.: 46 Cov.: 32 AF XY: 0.0211 AC XY: 1569 AN XY: 74490

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0632

Gnomad4 FIN AF: 0.00650

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0141 Hom.: 5

Bravo AF: 0.0191

Asia WGS AF: 0.0350 AC: 122 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	0.024
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs25812; hg19: chr5-102373592;