rs1633769

chr9-133003890-G-Cchr9-133003890-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/exons	MANE	UniProt

Ensembl

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