rs6593279

Variant names:

• chr7-55736277-G-A
• rs6593279

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 0.396 in 151,836 control chromosomes in the GnomAD database, including 17,421 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 0.40 (17421 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 11 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 = 0.791 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: 0.395 AC: 59992 AN: 151718 Hom.: 17379 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.396 AC: 60088 AN: 151836 Hom.: 17421 Cov.: 31 AF XY: 0.399 AC XY: 29612 AN XY: 74188

African (AFR) AF: 0.798 AC: 33064 AN: 41414

American (AMR) AF: 0.334 AC: 5086 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3267 AN: 5096

South Asian (SAS) AF: 0.446 AC: 2142 AN: 4798

European-Finnish (FIN) AF: 0.261 AC: 2755 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12268 AN: 67936

Other (OTH) AF: 0.344 AC: 727 AN: 2112

Alfa AF: 0.297 Hom.: 1349

Bravo AF: 0.418

Asia WGS AF: 0.527 AC: 1832 AN: 3476

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	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6593279; hg19: chr7-55803970;