chr4-120317331-A-C

Variant names:

• chr4-120317331-A-C
• rs2715953
• ENST00000504106.5:n.159-11202A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504106.5(MAD2L1-DT):​n.159-11202A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,984 control chromosomes in the GnomAD database, including 8,654 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 0.32 (8654 hom., cov: 32)
• Consequence: MAD2L1-DT ENST00000504106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504106.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAD2L1-DT	ENST00000504106.5	TSL:3	n.159-11202A>C		intron	N/A
	MAD2L1-DT	ENST00000508362.1	TSL:4	n.139-11202A>C		intron	N/A
	MAD2L1-DT	ENST00000653046.1		n.177-18307A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48625 AN: 151866 Hom.: 8652 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.320 AC: 48645 AN: 151984 Hom.: 8654 Cov.: 32 AF XY: 0.322 AC XY: 23949 AN XY: 74266

African (AFR) AF: 0.164 AC: 6784 AN: 41492

American (AMR) AF: 0.310 AC: 4728 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1452 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4816

European-Finnish (FIN) AF: 0.486 AC: 5120 AN: 10532

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26773 AN: 67936

Other (OTH) AF: 0.293 AC: 618 AN: 2106

Alfa AF: 0.343 Hom.: 1275

Bravo AF: 0.300

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.76
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs2715953; hg19: chr4-121238486;