rs11760455

Variant names:

• chr7-22108398-C-T
• rs11760455

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 0.404 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.533 AC: 22107 AN: 41464

American (AMR) AF: 0.396 AC: 6063 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1292 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1414 AN: 5170

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3189 AN: 10566

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24079 AN: 67970

Other (OTH) AF: 0.382 AC: 806 AN: 2112

Alfa AF: 0.379 Hom.: 22823

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11760455; hg19: chr7-22148016;