chr15-85824413-A-G

Variant names:

• chr15-85824413-A-G
• rs7170181

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 0.263 in 151,926 control chromosomes in the GnomAD database, including 6,141 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 (6141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.263 AC: 39912 AN: 151808 Hom.: 6119 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.263 AC: 39990 AN: 151926 Hom.: 6141 Cov.: 31 AF XY: 0.265 AC XY: 19704 AN XY: 74258

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.262

Alfa AF: 0.190 Hom.: 5058

Bravo AF: 0.275

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7170181; hg19: chr15-86367644;