18-50748035-C-T

Variant names:

• chr18-50748035-C-T
• rs1822458
• ENST00000761934.1:n.345+2244G>A

Variant summary

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

The ENST00000761934.1(ENSG00000299248):​n.345+2244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,122 control chromosomes in the GnomAD database, including 19,645 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 0.49 (19645 hom., cov: 33)
• Consequence: ENSG00000299248 ENST00000761934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 2 publications found

Genes affected

ENSG00000299248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761934.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299248	ENST00000761934.1		n.345+2244G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74502 AN: 152004 Hom.: 19645 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.490 AC: 74512 AN: 152122 Hom.: 19645 Cov.: 33 AF XY: 0.494 AC XY: 36765 AN XY: 74356

African (AFR) AF: 0.281 AC: 11664 AN: 41496

American (AMR) AF: 0.614 AC: 9390 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2242 AN: 5182

South Asian (SAS) AF: 0.594 AC: 2863 AN: 4818

European-Finnish (FIN) AF: 0.599 AC: 6332 AN: 10564

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38433 AN: 68000

Other (OTH) AF: 0.522 AC: 1099 AN: 2106

Alfa AF: 0.529 Hom.: 3881

Bravo AF: 0.481

Asia WGS AF: 0.524 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1822458; hg19: chr18-48274405;