rs2511469

chr11-68143516-T-Cchr11-68143516-T-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 0.585 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.606

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2511469; hg19: chr11-67910983;