rs4598087

Variant names:

• chr6-153603733-A-G
• rs4598087

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 0.337 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
• Publications: 3 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 = 0.777 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

African (AFR) AF: 0.784 AC: 32485 AN: 41422

American (AMR) AF: 0.226 AC: 3451 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3472

East Asian (EAS) AF: 0.0155 AC: 80 AN: 5158

South Asian (SAS) AF: 0.128 AC: 615 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10576

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11476 AN: 67982

Other (OTH) AF: 0.314 AC: 662 AN: 2106

Alfa AF: 0.380 Hom.: 8204

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
PhyloP100		0.070

Splicing

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

Other links and lift over

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