13-30908104-G-C

Position:

• chr13-30908104-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEDAG	NM_032849.4	c.278+1311G>C		intron_variant		ENST00000380482.9
TEX26-AS1	NR_038287.1	n.1437+22697C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEDAG	ENST00000380482.9	c.278+1311G>C		intron_variant		1	NM_032849.4	P1
TEX26-AS1	ENST00000585870.6	n.1437+22697C>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.389

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343945; hg19: chr13-31482241;