ENST00000640003.1:n.368+61152C>T

Variant names:

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

Variant summary

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

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640003.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284418	ENST00000640003.1	TSL:5	n.368+61152C>T		intron	N/A
	ENSG00000284418	ENST00000764217.1		n.118+61152C>T		intron	N/A
	ENSG00000284418	ENST00000764218.1		n.118+61152C>T		intron	N/A

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

African (AFR) AF: 0.829 AC: 34433 AN: 41520

American (AMR) AF: 0.802 AC: 12241 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2786 AN: 3464

East Asian (EAS) AF: 0.630 AC: 3245 AN: 5148

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4818

European-Finnish (FIN) AF: 0.828 AC: 8761 AN: 10580

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54255 AN: 67930

Other (OTH) AF: 0.794 AC: 1678 AN: 2114

Alfa AF: 0.798 Hom.: 43100

Bravo AF: 0.800

Asia WGS AF: 0.704 AC: 2447 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.70
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1463014; hg19: chr9-22944927;