18-73076929-A-G

Variant names:

• chr18-73076929-A-G
• rs2194633
• ENST00000815524.1:n.252+4627T>C

Variant summary

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

The ENST00000815524.1(ENSG00000306127):​n.252+4627T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,108 control chromosomes in the GnomAD database, including 10,185 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 0.35 (10185 hom., cov: 34)
• Consequence: ENSG00000306127 ENST00000815524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 4 publications found

Genes affected

ENSG00000306127 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 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
ENSG00000306127	ENST00000815524.1	n.252+4627T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52907 AN: 151990 Hom.: 10181 Cov.: 34

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.348 AC: 52915 AN: 152108 Hom.: 10185 Cov.: 34 AF XY: 0.346 AC XY: 25752 AN XY: 74354

African (AFR) AF: 0.190 AC: 7904 AN: 41532

American (AMR) AF: 0.319 AC: 4870 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2531 AN: 5162

South Asian (SAS) AF: 0.427 AC: 2056 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3796 AN: 10570

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28964 AN: 67966

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.399 Hom.: 49058

Bravo AF: 0.336

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.53
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2194633; hg19: chr18-70744164;