9-133175167-T-C

Variant names:

• chr9-133175167-T-C
• rs7850541

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 0.798 in 152,222 control chromosomes in the GnomAD database, including 48,675 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 0.80 (48675 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.798 AC: 121383 AN: 152104 Hom.: 48631 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.798 AC: 121482 AN: 152222 Hom.: 48675 Cov.: 33 AF XY: 0.802 AC XY: 59709 AN XY: 74432

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.770

Alfa AF: 0.775 Hom.: 6046

Bravo AF: 0.795

Asia WGS AF: 0.781 AC: 2714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7850541; hg19: chr9-136050554;