chr11-69462338-G-A

Variant names:

• chr11-69462338-G-A
• rs1938684

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 0.32 in 150,310 control chromosomes in the GnomAD database, including 10,360 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 0.32 (10360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 47966 AN: 150186 Hom.: 10316 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.320 AC: 48072 AN: 150310 Hom.: 10360 Cov.: 32 AF XY: 0.324 AC XY: 23781 AN XY: 73490

African (AFR) AF: 0.555 AC: 22766 AN: 41050

American (AMR) AF: 0.404 AC: 6129 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 420 AN: 3418

East Asian (EAS) AF: 0.696 AC: 3546 AN: 5098

South Asian (SAS) AF: 0.362 AC: 1715 AN: 4738

European-Finnish (FIN) AF: 0.200 AC: 2102 AN: 10518

Middle Eastern (MID) AF: 0.157 AC: 44 AN: 280

European-Non Finnish (NFE) AF: 0.159 AC: 10647 AN: 67056

Other (OTH) AF: 0.269 AC: 562 AN: 2086

Alfa AF: 0.204 Hom.: 7429

Bravo AF: 0.341

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.31
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1938684; hg19: chr11-69277106;