rs1550576

Variant names:

• chr15-57921216-C-T
• rs1550576

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 0.168 in 152,112 control chromosomes in the GnomAD database, including 2,242 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 0.17 (2242 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25548 AN: 151994 Hom.: 2242 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.168 AC: 25575 AN: 152112 Hom.: 2242 Cov.: 32 AF XY: 0.167 AC XY: 12401 AN XY: 74354

African (AFR) AF: 0.225 AC: 9324 AN: 41488

American (AMR) AF: 0.164 AC: 2511 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3468

East Asian (EAS) AF: 0.165 AC: 854 AN: 5166

South Asian (SAS) AF: 0.132 AC: 638 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1107 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9870 AN: 67986

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.156 Hom.: 5481

Bravo AF: 0.177

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.42
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1550576; hg19: chr15-58213414;