rs2511469

Variant names:

• chr11-68143516-T-C
• rs2511469

Your query was ambiguous. Multiple possible variants found:

• chr11-68143516-T-C
• chr11-68143516-T-G

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 0.585 in 151,858 control chromosomes in the GnomAD database, including 26,100 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 0.59 (26100 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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: 0.585 AC: 88786 AN: 151740 Hom.: 26076 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.585 AC: 88856 AN: 151858 Hom.: 26100 Cov.: 30 AF XY: 0.590 AC XY: 43765 AN XY: 74218

African (AFR) AF: 0.548 AC: 22674 AN: 41378

American (AMR) AF: 0.671 AC: 10233 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2146 AN: 3466

East Asian (EAS) AF: 0.667 AC: 3433 AN: 5144

South Asian (SAS) AF: 0.680 AC: 3281 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6281 AN: 10536

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38834 AN: 67944

Other (OTH) AF: 0.606 AC: 1275 AN: 2104

Alfa AF: 0.577 Hom.: 3158

Bravo AF: 0.594

Asia WGS AF: 0.660 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.16
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2511469; hg19: chr11-67910983;