rs35131064

Positions:

• chr6-44204326-C-T

Variant summary

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

The XM_024446300.2(MYMX):​c.-824C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,008 control chromosomes in the GnomAD database, including 3,283 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 0.19 (3283 hom., cov: 31)
• Consequence: MYMX XM_024446300.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

MYMX (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYMX	XM_024446300.2	c.-824C>T		5_prime_UTR_variant	2/4		XP_024302068.1
POLR1C	NM_001318876.2	c.946-237564C>T		intron_variant			NP_001305805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29461 AN: 151890 Hom.: 3285 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.194 AC: 29477 AN: 152008 Hom.: 3283 Cov.: 31 AF XY: 0.191 AC XY: 14154 AN XY: 74282

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.0232

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.231

Alfa AF: 0.221 Hom.: 946

Bravo AF: 0.188

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35131064; hg19: chr6-44172063;