rs11760455

Positions:

• chr7-22108398-C-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 0.404 in 152,088 control chromosomes in the GnomAD database, including 12,919 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 0.40 (12919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61367 AN: 151970 Hom.: 12900 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.404 AC: 61437 AN: 152088 Hom.: 12919 Cov.: 32 AF XY: 0.402 AC XY: 29920 AN XY: 74354

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.382

Alfa AF: 0.362 Hom.: 12225

Bravo AF: 0.413

Asia WGS AF: 0.353 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11760455; hg19: chr7-22148016;