rs6578246

Variant names:

• chr11-2224115-G-A
• rs6578246

Your query was ambiguous. Multiple possible variants found:

• chr11-2224115-G-A
• chr11-2224115-G-C
• chr11-2224115-G-T

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 0.922 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.897 AC: 37218 AN: 41502

American (AMR) AF: 0.777 AC: 11869 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3326 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4837 AN: 5168

South Asian (SAS) AF: 0.965 AC: 4663 AN: 4830

European-Finnish (FIN) AF: 0.944 AC: 9994 AN: 10588

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65291 AN: 68030

Other (OTH) AF: 0.936 AC: 1977 AN: 2112

Alfa AF: 0.917 Hom.: 11084

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6578246; hg19: chr11-2245345;