4-99118802-T-G

Variant names:

• chr4-99118802-T-G
• rs2602878
• ENST00000500358.6:n.429-14753T>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-14753T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,120 control chromosomes in the GnomAD database, including 48,624 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 0.79 (48624 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 4 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.429-14753T>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-14753T>G		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.426-14753T>G		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.481-14753T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120718 AN: 152002 Hom.: 48570 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.794 AC: 120833 AN: 152120 Hom.: 48624 Cov.: 32 AF XY: 0.802 AC XY: 59613 AN XY: 74364

African (AFR) AF: 0.896 AC: 37171 AN: 41486

American (AMR) AF: 0.799 AC: 12221 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5165 AN: 5174

South Asian (SAS) AF: 0.884 AC: 4258 AN: 4816

European-Finnish (FIN) AF: 0.773 AC: 8188 AN: 10592

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48951 AN: 67980

Other (OTH) AF: 0.766 AC: 1617 AN: 2110

Alfa AF: 0.726 Hom.: 42160

Bravo AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.83
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2602878; hg19: chr4-100039953;