chr4-120553417-A-G

Position:

• chr4-120553417-A-G

Variant summary

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

The ENST00000653046.1(MAD2L1-DT):​n.271-10894A>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 0.349 in 151,906 control chromosomes in the GnomAD database, including 10,540 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 0.35 (10540 hom., cov: 31)
• Consequence: MAD2L1-DT ENST00000653046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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.271-10894A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52967 AN: 151788 Hom.: 10532 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.349 AC: 52992 AN: 151906 Hom.: 10540 Cov.: 31 AF XY: 0.341 AC XY: 25295 AN XY: 74258

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.385

Alfa AF: 0.312 Hom.: 11492

Bravo AF: 0.361

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833652; hg19: chr4-121474572;