rs7113069

Variant names:

• chr11-56415530-G-A
• rs7113069

Your query was ambiguous. Multiple possible variants found:

• chr11-56415530-G-A
• chr11-56415530-G-C
• chr11-56415530-G-T

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 0.393 in 138,944 control chromosomes in the GnomAD database, including 11,000 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 0.39 (11000 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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: 0.393 AC: 54610 AN: 138840 Hom.: 10975 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.406

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.393 AC: 54646 AN: 138944 Hom.: 11000 Cov.: 31 AF XY: 0.403 AC XY: 27330 AN XY: 67860

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.430

Alfa AF: 0.295 Hom.: 1261

Bravo AF: 0.364

Asia WGS AF: 0.588 AC: 2039 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7113069; hg19: chr11-56183006;