rs748964

chr9-134442243-C-Gchr9-134442243-C-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 0.884 in 152,286 control chromosomes in the GnomAD database, including 59,814 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 0.88 (59814 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

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 (AFR) allele frequency at 95% confidence interval = 0.953 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: 0.884 AC: 134544 AN: 152168 Hom.: 59773 Cov.: 34

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.884 AC: 134641 AN: 152286 Hom.: 59814 Cov.: 34 AF XY: 0.882 AC XY: 65678 AN XY: 74454

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.846

Alfa AF: 0.881 Hom.: 6875

Bravo AF: 0.883

Asia WGS AF: 0.785 AC: 2731 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	0.028
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748964; hg19: chr9-137334089; COSMIC: COSV62683935;