18-10279359-A-G

Variant names:

• chr18-10279359-A-G
• rs16974035
• ENST00000826388.1:n.144-7886A>G

Variant summary

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

The ENST00000826388.1(ENSG00000287065):​n.144-7886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,134 control chromosomes in the GnomAD database, including 7,409 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 0.28 (7409 hom., cov: 33)
• Consequence: ENSG00000287065 ENST00000826388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 1 publications found

Genes affected

ENSG00000287065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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
ENSG00000287065	ENST00000826388.1	n.144-7886A>G		intron_variant	Intron 1 of 2
ENSG00000287065	ENST00000826389.1	n.134+17689A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42624 AN: 152016 Hom.: 7395 Cov.: 33

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.280 AC: 42649 AN: 152134 Hom.: 7409 Cov.: 33 AF XY: 0.285 AC XY: 21190 AN XY: 74370

African (AFR) AF: 0.0787 AC: 3269 AN: 41536

American (AMR) AF: 0.433 AC: 6617 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3472

East Asian (EAS) AF: 0.535 AC: 2760 AN: 5158

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3972 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22642 AN: 67968

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.286 Hom.: 3505

Bravo AF: 0.281

Asia WGS AF: 0.386 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.24
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs16974035; hg19: chr18-10279356;