rs11976165

chr7-56632861-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 0.218 in 152,082 control chromosomes in the GnomAD database, including 3,784 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 0.22 (3784 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33128 AN: 151964 Hom.: 3772 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0908

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.218 AC: 33164 AN: 152082 Hom.: 3784 Cov.: 33 AF XY: 0.217 AC XY: 16165 AN XY: 74346

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.200

Alfa AF: 0.213 Hom.: 600

Bravo AF: 0.227

Asia WGS AF: 0.174 AC: 604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.0
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11976165; hg19: chr7-56700554; COSMIC: COSV101466844;