chr7-132005923-G-T

Position:

• chr7-132005923-G-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 0.868 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;