rs598832

Variant names:

• chr6-153951483-G-A
• rs598832

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 0.883 in 152,174 control chromosomes in the GnomAD database, including 59,390 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 0.88 (59390 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.883 AC: 134218 AN: 152056 Hom.: 59337 Cov.: 31

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.883 AC: 134329 AN: 152174 Hom.: 59390 Cov.: 31 AF XY: 0.885 AC XY: 65871 AN XY: 74406

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.872

Alfa AF: 0.856 Hom.: 20869

Bravo AF: 0.885

Asia WGS AF: 0.906 AC: 3138 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs598832; hg19: chr6-154272618;