rs2036527

Variant names:

• chr15-78559273-G-A
• rs2036527

Your query was ambiguous. Multiple possible variants found:

• chr15-78559273-G-A
• chr15-78559273-G-C
• chr15-78559273-G-T

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 0.288 in 152,096 control chromosomes in the GnomAD database, including 6,845 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 0.29 (6845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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: 0.288 AC: 43709 AN: 151978 Hom.: 6838 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.288 AC: 43744 AN: 152096 Hom.: 6845 Cov.: 33 AF XY: 0.284 AC XY: 21105 AN XY: 74348

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.306

Alfa AF: 0.335 Hom.: 16215

Bravo AF: 0.277

Asia WGS AF: 0.134 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036527; hg19: chr15-78851615;