rs1633769

Variant names:

• chr9-133003890-G-C
• rs1633769

Your query was ambiguous. Multiple possible variants found:

• chr9-133003890-G-C
• chr9-133003890-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 0.615 in 152,170 control chromosomes in the GnomAD database, including 31,423 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 0.61 (31423 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 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: 0.615 AC: 93470 AN: 152050 Hom.: 31406 Cov.: 34

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.615 AC: 93510 AN: 152170 Hom.: 31423 Cov.: 34 AF XY: 0.617 AC XY: 45905 AN XY: 74384

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.657

Alfa AF: 0.658 Hom.: 4323

Bravo AF: 0.596

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1633769; hg19: chr9-135879277;