7-132005923-G-T

Variant names:

• chr7-132005923-G-T
• rs28699613

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 0.868 in 151,914 control chromosomes in the GnomAD database, including 57,419 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 0.87 (57419 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.868 AC: 131686 AN: 151796 Hom.: 57355 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.868 AC: 131813 AN: 151914 Hom.: 57419 Cov.: 31 AF XY: 0.869 AC XY: 64508 AN XY: 74236

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.853

Alfa AF: 0.856 Hom.: 7364

Bravo AF: 0.872

Asia WGS AF: 0.938 AC: 3239 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.93
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28699613; hg19: chr7-131690682;