rs6578592

Variant names:

• chr11-5247910-C-A
• rs6578592

Your query was ambiguous. Multiple possible variants found:

• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;