rs4088802

chr4-120544276-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653046.1(MAD2L1-DT):n.271-20035A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAD2L1-DT	ENST00000653046.1	n.271-20035A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.820

Alfa AF: 0.791 Hom.: 5915

Bravo AF: 0.780

Asia WGS AF: 0.667 AC: 2307 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	14
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4088802; hg19: chr4-121465431;