rs1463014

Variant names:

• chr9-22944928-G-A
• rs1463014
• ENST00000640003.1:n.368+61152C>T

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000640003.1(ENSG00000284418):​n.368+61152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

ENSG00000284418 (HGNC:58153):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284418	ENST00000640003.1	n.368+61152C>T		intron_variant	Intron 3 of 9	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;