chr11-69206503-A-G

Variant names:

• chr11-69206503-A-G
• rs4255548

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 0.628 in 150,090 control chromosomes in the GnomAD database, including 29,757 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 0.63 (29757 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.628 AC: 94124 AN: 149974 Hom.: 29725 Cov.: 27

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.628 AC: 94209 AN: 150090 Hom.: 29757 Cov.: 27 AF XY: 0.630 AC XY: 46072 AN XY: 73188

Gnomad4 AFR AF: 0.682 AC: 0.68189 AN: 0.68189

Gnomad4 AMR AF: 0.543 AC: 0.543418 AN: 0.543418

Gnomad4 ASJ AF: 0.735 AC: 0.735243 AN: 0.735243

Gnomad4 EAS AF: 0.465 AC: 0.465153 AN: 0.465153

Gnomad4 SAS AF: 0.547 AC: 0.547246 AN: 0.547246

Gnomad4 FIN AF: 0.671 AC: 0.671212 AN: 0.671212

Gnomad4 NFE AF: 0.620 AC: 0.620136 AN: 0.620136

Gnomad4 OTH AF: 0.642 AC: 0.641691 AN: 0.641691

Alfa AF: 0.620 Hom.: 109516

Bravo AF: 0.622

Asia WGS AF: 0.568 AC: 1916 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4255548; hg19: chr11-68973970;