rs900798

Variant names:

• chr15-74336729-T-G
• rs900798

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 0.562 in 152,140 control chromosomes in the GnomAD database, including 25,388 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 0.56 (25388 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 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: 0.562 AC: 85384 AN: 152020 Hom.: 25381 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.562 AC: 85432 AN: 152140 Hom.: 25388 Cov.: 33 AF XY: 0.557 AC XY: 41428 AN XY: 74382

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.543

Alfa AF: 0.642 Hom.: 41905

Bravo AF: 0.547

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs900798; hg19: chr15-74629070;