rs7025162

Variant names:

• chr9-133290774-T-C
• rs7025162

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 0.817 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.862 AC: 35771 AN: 41518

American (AMR) AF: 0.800 AC: 12221 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2908 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3237 AN: 5184

South Asian (SAS) AF: 0.760 AC: 3666 AN: 4822

European-Finnish (FIN) AF: 0.799 AC: 8461 AN: 10590

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55392 AN: 68002

Other (OTH) AF: 0.808 AC: 1708 AN: 2114

Alfa AF: 0.822 Hom.: 9092

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

Other links and lift over

dbSNP: rs7025162; hg19: chr9-136166346;