ENST00000640003.1:n.251-110404T>C

Variant names:

• chr9-23116601-A-G
• rs10511713
• ENST00000640003.1:n.251-110404T>C

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.251-110404T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 152,164 control chromosomes in the GnomAD database, including 63 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 0.014 (63 hom., cov: 32)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 0 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0607 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.251-110404T>C		intron_variant	Intron 2 of 9	5
ENSG00000284418	ENST00000664493.1	n.222-110404T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2202 AN: 152046 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.00762

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0665

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.00857

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0145 AC: 2200 AN: 152164 Hom.: 63 Cov.: 32 AF XY: 0.0163 AC XY: 1213 AN XY: 74386

African (AFR) AF: 0.00762 AC: 317 AN: 41576

American (AMR) AF: 0.0512 AC: 779 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3468

East Asian (EAS) AF: 0.0664 AC: 343 AN: 5162

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4824

European-Finnish (FIN) AF: 0.00857 AC: 91 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00505 AC: 343 AN: 67968

Other (OTH) AF: 0.0123 AC: 26 AN: 2108

Alfa AF: 0.0112 Hom.: 5

Bravo AF: 0.0160

Asia WGS AF: 0.0680 AC: 236 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.9
DANN	Benign	0.60
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10511713; hg19: chr9-23116600;