ENST00000640003.1:n.369-46346C>T

Variant names:

• chr9-22920665-G-A
• rs1017783
• ENST00000640003.1:n.369-46346C>T

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.369-46346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 150,114 control chromosomes in the GnomAD database, including 8,583 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 0.31 (8583 hom., cov: 30)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 12 publications found

Genes affected

ENSG00000284418 (HGNC:58153):

LOC105375990 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375990	XR_929515.2	n.5078-3161C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284418	ENST00000640003.1	n.369-46346C>T		intron_variant	Intron 3 of 9	5
ENSG00000284418	ENST00000764217.1	n.119-46346C>T		intron_variant	Intron 1 of 5
ENSG00000284418	ENST00000764218.1	n.119-46346C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.312 AC: 46760 AN: 149998 Hom.: 8581 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.312 AC: 46766 AN: 150114 Hom.: 8583 Cov.: 30 AF XY: 0.317 AC XY: 23167 AN XY: 73196

African (AFR) AF: 0.117 AC: 4757 AN: 40648

American (AMR) AF: 0.421 AC: 6318 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1404 AN: 3452

East Asian (EAS) AF: 0.158 AC: 796 AN: 5044

South Asian (SAS) AF: 0.346 AC: 1640 AN: 4738

European-Finnish (FIN) AF: 0.455 AC: 4695 AN: 10330

Middle Eastern (MID) AF: 0.406 AC: 116 AN: 286

European-Non Finnish (NFE) AF: 0.386 AC: 26109 AN: 67632

Other (OTH) AF: 0.325 AC: 672 AN: 2070

Alfa AF: 0.354 Hom.: 7618

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.40
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1017783; hg19: chr9-22920664;