rs1443658

Variant names:

• chr15-79094024-A-G
• rs1443658

Your query was ambiguous. Multiple possible variants found:

• chr15-79094024-A-G
• chr15-79094024-A-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 0.522 in 151,824 control chromosomes in the GnomAD database, including 22,826 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 0.52 (22826 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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: 0.522 AC: 79163 AN: 151706 Hom.: 22776 Cov.: 30

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.522 AC: 79278 AN: 151824 Hom.: 22826 Cov.: 30 AF XY: 0.518 AC XY: 38467 AN XY: 74214

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.481

Alfa AF: 0.393 Hom.: 2825

Bravo AF: 0.554

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443658; hg19: chr15-79386366;