chr15-39552114-G-A

Variant names:

• chr15-39552114-G-A
• rs2618157

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 0.242 in 152,152 control chromosomes in the GnomAD database, including 9,320 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 0.24 (9320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 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: 0.242 AC: 36774 AN: 152034 Hom.: 9279 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.0525

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.242 AC: 36872 AN: 152152 Hom.: 9320 Cov.: 32 AF XY: 0.232 AC XY: 17271 AN XY: 74396

African (AFR) AF: 0.648 AC: 26859 AN: 41458

American (AMR) AF: 0.123 AC: 1884 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3472

East Asian (EAS) AF: 0.00811 AC: 42 AN: 5178

South Asian (SAS) AF: 0.0522 AC: 252 AN: 4830

European-Finnish (FIN) AF: 0.0601 AC: 637 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0923 AC: 6280 AN: 68004

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.141 Hom.: 8319

Bravo AF: 0.264

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.20
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2618157; hg19: chr15-39844315;