rs6578246

chr11-2224115-G-Achr11-2224115-G-Cchr11-2224115-G-T

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 0.922 in 152,180 control chromosomes in the GnomAD database, including 65,059 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 0.92 (65059 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.954 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: 0.922 AC: 140262 AN: 152060 Hom.: 65009 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.922 AC: 140365 AN: 152180 Hom.: 65059 Cov.: 31 AF XY: 0.919 AC XY: 68402 AN XY: 74400

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.936

Alfa AF: 0.917 Hom.: 10762

Bravo AF: 0.908

Asia WGS AF: 0.941 AC: 3272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6578246; hg19: chr11-2245345;