rs4275319

chr9-63917891-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;