rs4275319

Variant names:

• chr9-63917891-G-A
• rs4275319

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 0.341 in 142,770 control chromosomes in the GnomAD database, including 9,288 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 0.34 (9288 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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: 0.341 AC: 48654 AN: 142644 Hom.: 9245 Cov.: 34

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.341 AC: 48750 AN: 142770 Hom.: 9288 Cov.: 34 AF XY: 0.343 AC XY: 23918 AN XY: 69718

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.347

Alfa AF: 0.192 Hom.: 2153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4275319; hg19: chr9-68513625;