rs1872939

Positions:

• chr4-120551439-A-G
• chr4-120551439-A-T

Variant summary

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

The ENST00000653046.1(MAD2L1-DT):​n.271-12872A>G 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 0.786 in 152,200 control chromosomes in the GnomAD database, including 47,131 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 (47131 hom., cov: 33)
• Consequence: MAD2L1-DT ENST00000653046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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=-0.88).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAD2L1-DT	ENST00000653046.1	n.271-12872A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119545 AN: 152082 Hom.: 47104 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.786 AC: 119622 AN: 152200 Hom.: 47131 Cov.: 33 AF XY: 0.787 AC XY: 58529 AN XY: 74402

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.828

Alfa AF: 0.790 Hom.: 6014

Bravo AF: 0.788

Asia WGS AF: 0.667 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872939; hg19: chr4-121472594;