rs1463014

Positions:

• chr9-22944928-G-A
• chr9-22944928-G-C
• chr9-22944928-G-T

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 0.803 in 152,038 control chromosomes in the GnomAD database, including 49,052 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 0.80 (49052 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

(HGNC:):

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 = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22944928G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284418	ENST00000640003.1	n.368+61152C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121960 AN: 151922 Hom.: 49015 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.803 AC: 122055 AN: 152038 Hom.: 49052 Cov.: 32 AF XY: 0.802 AC XY: 59578 AN XY: 74314

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.794

Alfa AF: 0.798 Hom.: 36659

Bravo AF: 0.800

Asia WGS AF: 0.704 AC: 2447 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463014; hg19: chr9-22944927;