chr11-69547646-A-G

Variant names:

• chr11-69547646-A-G
• rs1485993

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 0.49 in 152,076 control chromosomes in the GnomAD database, including 21,091 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 0.49 (21091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.490 AC: 74449 AN: 151958 Hom.: 21092 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.490 AC: 74459 AN: 152076 Hom.: 21091 Cov.: 32 AF XY: 0.489 AC XY: 36378 AN XY: 74334

African (AFR) AF: 0.228 AC: 9462 AN: 41498

American (AMR) AF: 0.413 AC: 6304 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1784 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1206 AN: 5170

South Asian (SAS) AF: 0.502 AC: 2422 AN: 4822

European-Finnish (FIN) AF: 0.740 AC: 7814 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43667 AN: 67964

Other (OTH) AF: 0.477 AC: 1008 AN: 2112

Alfa AF: 0.598 Hom.: 57997

Bravo AF: 0.452

Asia WGS AF: 0.374 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.33
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1485993; hg19: chr11-69362414;