rs6590281

Variant names:

• chr11-127849643-G-A
• rs6590281

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 0.263 in 151,920 control chromosomes in the GnomAD database, including 5,914 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 0.26 (5914 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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: 0.263 AC: 39914 AN: 151802 Hom.: 5913 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.263 AC: 39947 AN: 151920 Hom.: 5914 Cov.: 31 AF XY: 0.257 AC XY: 19098 AN XY: 74242

African (AFR) AF: 0.407 AC: 16851 AN: 41388

American (AMR) AF: 0.245 AC: 3747 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3468

East Asian (EAS) AF: 0.155 AC: 803 AN: 5166

South Asian (SAS) AF: 0.191 AC: 919 AN: 4808

European-Finnish (FIN) AF: 0.228 AC: 2406 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 60 AN: 290

European-Non Finnish (NFE) AF: 0.202 AC: 13750 AN: 67936

Other (OTH) AF: 0.267 AC: 564 AN: 2116

Alfa AF: 0.220 Hom.: 17058

Bravo AF: 0.275

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.59
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6590281; hg19: chr11-127719538;