rs4088802

Variant names:

• chr4-120544276-A-C
• rs4088802
• ENST00000653046.1:n.271-20035A>C

Variant summary

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

The ENST00000653046.1(MAD2L1-DT):​n.271-20035A>C 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 152,138 control chromosomes in the GnomAD database, including 46,444 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 (46444 hom., cov: 34)
• Consequence: MAD2L1-DT ENST00000653046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653046.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAD2L1-DT	ENST00000653046.1		n.271-20035A>C		intron	N/A
	MAD2L1-DT	ENST00000740075.1		n.78-18144A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118598 AN: 152020 Hom.: 46413 Cov.: 34

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.780 AC: 118682 AN: 152138 Hom.: 46444 Cov.: 34 AF XY: 0.780 AC XY: 58023 AN XY: 74350

African (AFR) AF: 0.751 AC: 31177 AN: 41508

American (AMR) AF: 0.822 AC: 12577 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3169 AN: 3468

East Asian (EAS) AF: 0.567 AC: 2927 AN: 5166

South Asian (SAS) AF: 0.756 AC: 3646 AN: 4820

European-Finnish (FIN) AF: 0.816 AC: 8624 AN: 10570

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

European-Non Finnish (NFE) AF: 0.791 AC: 53783 AN: 67990

Other (OTH) AF: 0.820 AC: 1731 AN: 2112

Alfa AF: 0.791 Hom.: 6154

Bravo AF: 0.780

Asia WGS AF: 0.667 AC: 2307 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		0.96

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4088802;

hg19: chr4-121465431;