rs1443015

Variant names:

• chr18-30516836-T-C
• rs1443015

Your query was ambiguous. Multiple possible variants found:

• chr18-30516836-T-C
• chr18-30516836-T-G

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 0.352 in 151,976 control chromosomes in the GnomAD database, including 9,674 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 0.35 (9674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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 = 0.376 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: 0.352 AC: 53407 AN: 151860 Hom.: 9661 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.352 AC: 53455 AN: 151976 Hom.: 9674 Cov.: 32 AF XY: 0.347 AC XY: 25743 AN XY: 74272

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.322

Alfa AF: 0.351 Hom.: 15633

Bravo AF: 0.339

Asia WGS AF: 0.239 AC: 831 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	5.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443015; hg19: chr18-28096802;