7-133222893-A-G

Variant names:

• chr7-133222893-A-G
• rs11979455

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 0.35 in 151,958 control chromosomes in the GnomAD database, including 11,473 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 0.35 (11473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.350 AC: 53114 AN: 151840 Hom.: 11450 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.350 AC: 53181 AN: 151958 Hom.: 11473 Cov.: 32 AF XY: 0.348 AC XY: 25845 AN XY: 74276

African (AFR) AF: 0.607 AC: 25136 AN: 41392

American (AMR) AF: 0.230 AC: 3513 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2655 AN: 5146

South Asian (SAS) AF: 0.359 AC: 1723 AN: 4800

European-Finnish (FIN) AF: 0.218 AC: 2313 AN: 10586

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16060 AN: 67978

Other (OTH) AF: 0.342 AC: 720 AN: 2106

Alfa AF: 0.273 Hom.: 19849

Bravo AF: 0.359

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.39
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs11979455; hg19: chr7-132907651;