18-10321513-T-C

Variant names:

• chr18-10321513-T-C
• rs206625
• ENST00000666410.1:n.1039-43A>G

Variant summary

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

The ENST00000666410.1(ENSG00000264876):​n.1039-43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,060 control chromosomes in the GnomAD database, including 17,397 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 0.45 (17397 hom., cov: 32)
• Consequence: ENSG00000264876 ENST00000666410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 1 publications found

Genes affected

ENSG00000264876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371985	XR_001753344.2	n.532+635A>G		intron_variant	Intron 3 of 4
LOC105371985	XR_001753345.2	n.533-43A>G		intron_variant	Intron 3 of 3
LOC105371985	XR_001753346.2	n.463+635A>G		intron_variant	Intron 2 of 3
LOC105371985	XR_007066287.1	n.432-43A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264876	ENST00000666410.1	n.1039-43A>G		intron_variant	Intron 6 of 6
ENSG00000287065	ENST00000669383.1	n.401-1510T>C		intron_variant	Intron 2 of 2
ENSG00000287065	ENST00000826388.1	n.214-1510T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68833 AN: 151942 Hom.: 17398 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.453 AC: 68859 AN: 152060 Hom.: 17397 Cov.: 32 AF XY: 0.455 AC XY: 33813 AN XY: 74312

African (AFR) AF: 0.210 AC: 8728 AN: 41506

American (AMR) AF: 0.552 AC: 8442 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2030 AN: 3466

East Asian (EAS) AF: 0.682 AC: 3519 AN: 5158

South Asian (SAS) AF: 0.432 AC: 2081 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5701 AN: 10572

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36749 AN: 67950

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.499 Hom.: 10520

Bravo AF: 0.448

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs206625; hg19: chr18-10321510;