rs590523

Positions:

• chr6-137629740-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 0.194 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

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 (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.194 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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.209

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs590523; hg19: chr6-137950877;