9-134444068-C-G

Variant names:

• chr9-134444068-C-G
• rs1007971

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 0.669 in 151,906 control chromosomes in the GnomAD database, including 36,108 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 0.67 (36108 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 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: 0.670 AC: 101659 AN: 151790 Hom.: 36110 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.669 AC: 101687 AN: 151906 Hom.: 36108 Cov.: 30 AF XY: 0.672 AC XY: 49878 AN XY: 74232

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.669

Alfa AF: 0.673 Hom.: 2292

Bravo AF: 0.650

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007971; hg19: chr9-137335914; COSMIC: COSV62683938;