ENST00000640003.1:n.491-20118C>T

Variant names:

• chr9-22842203-G-A
• rs12554707
• ENST00000640003.1:n.491-20118C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640003.1(ENSG00000284418):​n.491-20118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 151,986 control chromosomes in the GnomAD database, including 744 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 0.081 (744 hom., cov: 33)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.147 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.491-20118C>T		intron_variant	Intron 4 of 9	5
ENSG00000284418	ENST00000764217.1	n.240+31995C>T		intron_variant	Intron 2 of 5
ENSG00000284418	ENST00000764218.1	n.240+31995C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12253 AN: 151868 Hom.: 745 Cov.: 33

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0806 AC: 12256 AN: 151986 Hom.: 744 Cov.: 33 AF XY: 0.0863 AC XY: 6413 AN XY: 74300

African (AFR) AF: 0.0189 AC: 783 AN: 41516

American (AMR) AF: 0.152 AC: 2317 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5168

South Asian (SAS) AF: 0.0876 AC: 422 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1825 AN: 10536

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6436 AN: 67912

Other (OTH) AF: 0.0678 AC: 143 AN: 2108

Alfa AF: 0.0733 Hom.: 254

Bravo AF: 0.0743

Asia WGS AF: 0.0460 AC: 160 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.77
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs12554707; hg19: chr9-22842202;