rs748964

Variant names:

• chr9-134442243-C-G
• rs748964

Your query was ambiguous. Multiple possible variants found:

• chr9-134442243-C-G
• chr9-134442243-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;