rs9329034

Variant names:

• chr4-68776903-T-C
• rs9329034

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 0.251 in 149,790 control chromosomes in the GnomAD database, including 8,285 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 0.25 (8285 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.251 AC: 37556 AN: 149674 Hom.: 8256 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.251 AC: 37637 AN: 149790 Hom.: 8285 Cov.: 31 AF XY: 0.245 AC XY: 18134 AN XY: 74038

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0716

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.222

Alfa AF: 0.180 Hom.: 606

Bravo AF: 0.275

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9329034; hg19: chr4-69642621;