chr11-69290824-A-G

Variant names:

• chr11-69290824-A-G
• rs7118561

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 0.3 in 152,142 control chromosomes in the GnomAD database, including 9,101 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 0.30 (9101 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.300 AC: 45567 AN: 152024 Hom.: 9088 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.300 AC: 45624 AN: 152142 Hom.: 9101 Cov.: 33 AF XY: 0.303 AC XY: 22569 AN XY: 74384

African (AFR) AF: 0.560 AC: 23236 AN: 41472

American (AMR) AF: 0.209 AC: 3202 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2156 AN: 5176

South Asian (SAS) AF: 0.369 AC: 1781 AN: 4824

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10592

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11695 AN: 67988

Other (OTH) AF: 0.277 AC: 586 AN: 2114

Alfa AF: 0.209 Hom.: 4315

Bravo AF: 0.306

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs7118561; hg19: chr11-69058291;