rs7118561

Positions:

• chr11-69290824-A-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 0.3 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.69290824A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.277

Alfa AF: 0.194 Hom.: 2660

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7118561; hg19: chr11-69058291;