9-110609627-G-A

Variant names:

• chr9-110609627-G-A
• rs4314720

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.577 AC: 23894 AN: 41416

American (AMR) AF: 0.802 AC: 12267 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5075 AN: 5178

South Asian (SAS) AF: 0.823 AC: 3963 AN: 4816

European-Finnish (FIN) AF: 0.887 AC: 9403 AN: 10602

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.782 AC: 53196 AN: 67996

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.764 Hom.: 7557

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4314720; hg19: chr9-113371907;