rs598832

Positions:

• chr6-153951483-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;