rs598832

Variant names:

• chr6-153951483-G-A
• rs598832

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.931 AC: 38675 AN: 41526

American (AMR) AF: 0.893 AC: 13664 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2915 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4813 AN: 5184

South Asian (SAS) AF: 0.881 AC: 4251 AN: 4826

European-Finnish (FIN) AF: 0.897 AC: 9490 AN: 10576

Middle Eastern (MID) AF: 0.729 AC: 210 AN: 288

European-Non Finnish (NFE) AF: 0.848 AC: 57641 AN: 67984

Other (OTH) AF: 0.872 AC: 1840 AN: 2110

Alfa AF: 0.857 Hom.: 24012

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs598832; hg19: chr6-154272618;