chr15-89984780-G-T

Variant names:

• chr15-89984780-G-T
• rs1256840

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 0.0751 in 152,186 control chromosomes in the GnomAD database, including 627 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 0.075 (627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11440 AN: 152068 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0751 AC: 11432 AN: 152186 Hom.: 627 Cov.: 32 AF XY: 0.0722 AC XY: 5372 AN XY: 74412

African (AFR) AF: 0.0196 AC: 815 AN: 41546

American (AMR) AF: 0.0622 AC: 951 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4820

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10602

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7926 AN: 67976

Other (OTH) AF: 0.0761 AC: 160 AN: 2102

Alfa AF: 0.0704 Hom.: 260

Bravo AF: 0.0718

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1256840; hg19: chr15-90528012;