rs1057745

Positions:

• chr19-39397750-G-A
• chr19-39397750-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_017592.4(MED29):​c.*51G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000978 in 1,431,764 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000098 (0 hom.)
• Consequence: MED29 NM_017592.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

MED29 (HGNC:23074): (mediator complex subunit 29) MED29 is a subunit of the Mediator complex, a multiprotein coactivator of RNA transcription that interacts with DNA-bound transcriptional activators, RNA polymerase II (see MIM 180660), and general initiation factors (Sato et al., 2003 [PubMed 14576168]).[supplied by OMIM, Aug 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.34673133).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MED29	NM_017592.4	c.*51G>A		3_prime_UTR_variant	4/4	ENST00000315588.11	NP_060062.2
MED29	NM_001317770.3	c.584G>A	p.Arg195Lys	missense_variant	4/4		NP_001304699.2
MED29	NR_133915.3	n.640G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED29	ENST00000315588.11	c.*51G>A		3_prime_UTR_variant	4/4	1	NM_017592.4	ENSP00000314343	P1
MED29	ENST00000615911.4	c.*51G>A		3_prime_UTR_variant	4/4	1		ENSP00000481733
MED29	ENST00000594368.5	c.584G>A	p.Arg195Lys	missense_variant	4/4	2		ENSP00000472501
MED29	ENST00000599417.2	c.*367G>A		3_prime_UTR_variant, NMD_transcript_variant	3/3	2		ENSP00000471101

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000134 AC: 3 AN: 223090 Hom.: 0 AF XY: 0.0000247 AC XY: 3 AN XY: 121674

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000688

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000957

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000978 AC: 14 AN: 1431764 Hom.: 0 Cov.: 32 AF XY: 0.0000183 AC XY: 13 AN XY: 710130

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000106

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000363

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ExAC AF: 0.0000330 AC: 4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	10
DANN	Benign	0.78
FATHMM_MKL	Benign	0.25	N
LIST_S2	Benign	0.16	T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.35	T
MutationTaster	Benign	9.5e-16	P
PrimateAI	Benign	0.30	T
Vest4		0.069
MVP		0.57
GERP RS		4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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: rs1057745; hg19: chr19-39888390;