15-37120771-A-G

Variant names:

• chr15-37120771-A-G
• rs2381966

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 0.257 in 152,116 control chromosomes in the GnomAD database, including 5,315 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 0.26 (5315 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.889

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.257 AC: 39121 AN: 151998 Hom.: 5312 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.257 AC: 39141 AN: 152116 Hom.: 5315 Cov.: 33 AF XY: 0.253 AC XY: 18837 AN XY: 74364

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.00578

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.221

Alfa AF: 0.253 Hom.: 2186

Bravo AF: 0.250

Asia WGS AF: 0.107 AC: 376 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381966; hg19: chr15-37412972;