rs900798

Variant names:

• chr15-74336729-T-G
• rs900798

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.364 AC: 15092 AN: 41504

American (AMR) AF: 0.591 AC: 9039 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2115 AN: 5160

South Asian (SAS) AF: 0.447 AC: 2153 AN: 4820

European-Finnish (FIN) AF: 0.692 AC: 7336 AN: 10604

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45975 AN: 67968

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.634 Hom.: 51963

Bravo AF: 0.547

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.80
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs900798; hg19: chr15-74629070;