rs7025162

chr9-133290774-T-C

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 0.817 in 152,184 control chromosomes in the GnomAD database, including 51,138 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 0.82 (51138 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.817 AC: 124297 AN: 152068 Hom.: 51089 Cov.: 33

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.817 AC: 124395 AN: 152184 Hom.: 51138 Cov.: 33 AF XY: 0.813 AC XY: 60523 AN XY: 74404

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.808

Alfa AF: 0.821 Hom.: 6012

Bravo AF: 0.821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7025162; hg19: chr9-136166346;