rs900798

chr15-74336729-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;