rs4314720

chr9-110609627-G-Achr9-110609627-G-C

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 0.743 in 152,082 control chromosomes in the GnomAD database, including 42,984 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 0.74 (42984 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.743 AC: 112874 AN: 151964 Hom.: 42946 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.743 AC: 112964 AN: 152082 Hom.: 42984 Cov.: 32 AF XY: 0.750 AC XY: 55733 AN XY: 74348

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.746

Alfa AF: 0.770 Hom.: 7435

Bravo AF: 0.730

Asia WGS AF: 0.880 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4314720; hg19: chr9-113371907;