rs1883468

Variant names:

• chr6-138155894-A-C
• rs1883468

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 0.502 in 152,068 control chromosomes in the GnomAD database, including 19,836 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 0.50 (19836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.502 AC: 76310 AN: 151950 Hom.: 19793 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.502 AC: 76397 AN: 152068 Hom.: 19836 Cov.: 33 AF XY: 0.500 AC XY: 37165 AN XY: 74332

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.485

Alfa AF: 0.452 Hom.: 32290

Bravo AF: 0.516

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883468; hg19: chr6-138477031;