rs590523

Variant names:

• chr6-137629740-G-A
• rs590523

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 0.194 in 151,382 control chromosomes in the GnomAD database, including 3,187 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 0.19 (3187 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.194 AC: 29392 AN: 151264 Hom.: 3186 Cov.: 29

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.194 AC: 29409 AN: 151382 Hom.: 3187 Cov.: 29 AF XY: 0.188 AC XY: 13921 AN XY: 73920

African (AFR) AF: 0.111 AC: 4578 AN: 41242

American (AMR) AF: 0.242 AC: 3671 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3464

East Asian (EAS) AF: 0.179 AC: 917 AN: 5134

South Asian (SAS) AF: 0.118 AC: 563 AN: 4780

European-Finnish (FIN) AF: 0.125 AC: 1303 AN: 10458

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16601 AN: 67856

Other (OTH) AF: 0.209 AC: 437 AN: 2092

Alfa AF: 0.211 Hom.: 603

Bravo AF: 0.205

Asia WGS AF: 0.153 AC: 531 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	1.5
DANN	Benign	0.60
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs590523; hg19: chr6-137950877;