4-120549894-C-T

Variant names:

• chr4-120549894-C-T
• rs2390024
• ENST00000653046.1:n.271-14417C>T

Variant summary

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

The ENST00000653046.1(MAD2L1-DT):​n.271-14417C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,184 control chromosomes in the GnomAD database, including 46,441 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 0.78 (46441 hom., cov: 33)
• Consequence: MAD2L1-DT ENST00000653046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 2 publications found

Genes affected

MAD2L1-DT (HGNC:55546): (MAD2L1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 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
MAD2L1-DT	ENST00000653046.1	n.271-14417C>T		intron_variant	Intron 2 of 2
MAD2L1-DT	ENST00000740075.1	n.78-12526C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118615 AN: 152066 Hom.: 46410 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.780 AC: 118698 AN: 152184 Hom.: 46441 Cov.: 33 AF XY: 0.780 AC XY: 58046 AN XY: 74412

African (AFR) AF: 0.751 AC: 31164 AN: 41496

American (AMR) AF: 0.822 AC: 12583 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3173 AN: 3472

East Asian (EAS) AF: 0.566 AC: 2921 AN: 5164

South Asian (SAS) AF: 0.756 AC: 3652 AN: 4828

European-Finnish (FIN) AF: 0.815 AC: 8633 AN: 10588

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53793 AN: 68020

Other (OTH) AF: 0.821 AC: 1732 AN: 2110

Alfa AF: 0.793 Hom.: 25718

Bravo AF: 0.780

Asia WGS AF: 0.668 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.40
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2390024; hg19: chr4-121471049;