rs4598087

Variant names:

• chr6-153603733-A-G
• rs4598087

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 0.337 in 151,988 control chromosomes in the GnomAD database, including 14,621 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 0.34 (14621 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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 = 0.777 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: 0.337 AC: 51146 AN: 151870 Hom.: 14576 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0155

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.337 AC: 51244 AN: 151988 Hom.: 14621 Cov.: 31 AF XY: 0.329 AC XY: 24417 AN XY: 74288

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.314

Alfa AF: 0.244 Hom.: 1708

Bravo AF: 0.365

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4598087; hg19: chr6-153924868; COSMIC: COSV60293680;