rs2618157

Variant names:

• chr15-39552114-G-A
• rs2618157

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 0.242 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00811

Gnomad4 SAS AF: 0.0522

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.199

Alfa AF: 0.109 Hom.: 2861

Bravo AF: 0.264

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2618157; hg19: chr15-39844315;