rs1595963

chr18-29880383-G-C

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 0.041 in 152,134 control chromosomes in the GnomAD database, including 189 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 0.041 (189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6228 AN: 152016 Hom.: 187 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0410 AC: 6240 AN: 152134 Hom.: 189 Cov.: 32 AF XY: 0.0406 AC XY: 3018 AN XY: 74350

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0462

Gnomad4 ASJ AF: 0.0181

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0248

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0314 Hom.: 22

Bravo AF: 0.0462

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1595963; hg19: chr18-27460348;