rs6578592

Positions:

• chr11-5247910-C-A
• chr11-5247910-C-G

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 0.823 in 152,146 control chromosomes in the GnomAD database, including 51,752 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 0.82 (51752 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5247910C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125073 AN: 152028 Hom.: 51694 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.823 AC: 125193 AN: 152146 Hom.: 51752 Cov.: 32 AF XY: 0.818 AC XY: 60843 AN XY: 74360

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.848

Alfa AF: 0.799 Hom.: 6518

Bravo AF: 0.838

Asia WGS AF: 0.862 AC: 2996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.82
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6578592; hg19: chr11-5269140;