4-99475533-G-T

Variant names:

• chr4-99475533-G-T
• rs2654849
• ENST00000506494.1:n.242+1215C>A

Variant summary

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

The ENST00000506494.1(ENSG00000250300):​n.242+1215C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,756 control chromosomes in the GnomAD database, including 25,704 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 0.58 (25704 hom., cov: 31)
• Consequence: ENSG00000250300 ENST00000506494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

ENSG00000250300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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
ENSG00000250300	ENST00000506494.1	n.242+1215C>A		intron_variant	Intron 2 of 3	6

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87552 AN: 151638 Hom.: 25686 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.577 AC: 87624 AN: 151756 Hom.: 25704 Cov.: 31 AF XY: 0.579 AC XY: 42945 AN XY: 74200

African (AFR) AF: 0.503 AC: 20791 AN: 41308

American (AMR) AF: 0.583 AC: 8882 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1989 AN: 5160

South Asian (SAS) AF: 0.428 AC: 2056 AN: 4806

European-Finnish (FIN) AF: 0.678 AC: 7154 AN: 10546

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42750 AN: 67910

Other (OTH) AF: 0.548 AC: 1155 AN: 2106

Alfa AF: 0.596 Hom.: 13909

Bravo AF: 0.569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.50
DANN	Benign	0.15
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2654849; hg19: chr4-100396690;