rs1493682

Positions:

• chr4-120120131-T-G

Variant summary

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

The ENST00000701263.1(MAD2L1-DT):​n.86-30412T>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 0.0865 in 152,014 control chromosomes in the GnomAD database, including 912 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 0.086 (912 hom., cov: 32)
• Consequence: MAD2L1-DT ENST00000701263.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

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 (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAD2L1-DT	XR_005976914.2	n.167-30412T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAD2L1-DT	ENST00000701263.1	n.86-30412T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13154 AN: 151896 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0865 AC: 13147 AN: 152014 Hom.: 912 Cov.: 32 AF XY: 0.0913 AC XY: 6787 AN XY: 74308

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0935 Hom.: 1154

Bravo AF: 0.0775

Asia WGS AF: 0.235 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493682; hg19: chr4-121041286;