rs17083008

chr6-152746792-G-A

Variant summary

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

The XR_007059337.1(MYCT1):n.2375G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,018 control chromosomes in the GnomAD database, including 8,223 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 0.28 (8223 hom., cov: 33)
• Consequence: MYCT1 XR_007059337.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

MYCT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYCT1	XR_007059337.1	n.2375G>A		non_coding_transcript_exon_variant	5/5
MYCT1	XR_007059338.1	n.2137G>A		non_coding_transcript_exon_variant	4/4
MYCT1	XR_007059339.1	n.2217G>A		non_coding_transcript_exon_variant	5/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42978 AN: 151900 Hom.: 8183 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.283 AC: 43066 AN: 152018 Hom.: 8223 Cov.: 33 AF XY: 0.279 AC XY: 20723 AN XY: 74326

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.283

Alfa AF: 0.237 Hom.: 684

Bravo AF: 0.294

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.74
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17083008; hg19: chr6-153067927;