13-30908104-G-C

Variant names:

• chr13-30908104-G-C
• rs1343945
• NM_032849.4:c.278+1311G>C

Variant summary

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

The NM_032849.4(MEDAG):​c.278+1311G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,078 control chromosomes in the GnomAD database, including 12,851 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 0.41 (12851 hom., cov: 33)
• Consequence: MEDAG NM_032849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 5 publications found

Genes affected

MEDAG (HGNC:25926): (mesenteric estrogen dependent adipogenesis) Predicted to be involved in positive regulation of fat cell differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TEX26-AS1 (HGNC:42784): (TEX26 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032849.4. 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
	MEDAG	NM_032849.4	MANE Select	c.278+1311G>C		intron	N/A	NP_116238.3
	TEX26-AS1	NR_038287.1		n.1437+22697C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEDAG	ENST00000380482.9	TSL:1 MANE Select	c.278+1311G>C		intron	N/A	ENSP00000369849.4
	MEDAG	ENST00000428944.1	TSL:5	c.86+1311G>C		intron	N/A	ENSP00000416838.1
	TEX26-AS1	ENST00000585870.6	TSL:2	n.1437+22697C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61875 AN: 151962 Hom.: 12844 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.407 AC: 61912 AN: 152078 Hom.: 12851 Cov.: 33 AF XY: 0.409 AC XY: 30386 AN XY: 74330

African (AFR) AF: 0.391 AC: 16214 AN: 41474

American (AMR) AF: 0.430 AC: 6569 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3464

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5176

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4822

European-Finnish (FIN) AF: 0.515 AC: 5446 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28013 AN: 67962

Other (OTH) AF: 0.389 AC: 823 AN: 2116

Alfa AF: 0.428 Hom.: 1769

Bravo AF: 0.399

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.41
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1343945; hg19: chr13-31482241;