rs2045325

Variant names:

• chr15-97170536-G-A
• rs2045325

Your query was ambiguous. Multiple possible variants found:

• chr15-97170536-G-A
• chr15-97170536-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 0.447 in 152,030 control chromosomes in the GnomAD database, including 15,447 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 0.45 (15447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.447 AC: 67876 AN: 151912 Hom.: 15441 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.447 AC: 67919 AN: 152030 Hom.: 15447 Cov.: 32 AF XY: 0.450 AC XY: 33434 AN XY: 74288

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.449

Alfa AF: 0.465 Hom.: 22037

Bravo AF: 0.436

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2045325; hg19: chr15-97713766; COSMIC: COSV56529586;