rs1362595

chr4-120094922-A-T

Variant summary

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

The ENST00000701263.1(MAD2L1-DT):n.85+11591A>T 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 0.219 in 152,134 control chromosomes in the GnomAD database, including 4,046 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 0.22 (4046 hom., cov: 32)
• Consequence: MAD2L1-DT ENST00000701263.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAD2L1-DT	XR_005976914.2	n.166+11591A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAD2L1-DT	ENST00000701263.1	n.85+11591A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33244 AN: 152016 Hom.: 4045 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.219 AC: 33243 AN: 152134 Hom.: 4046 Cov.: 32 AF XY: 0.217 AC XY: 16124 AN XY: 74380

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.229

Alfa AF: 0.240 Hom.: 601

Bravo AF: 0.212

Asia WGS AF: 0.207 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362595; hg19: chr4-121016077;