rs1443658

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;