rs17083008

Variant names:

• chr6-152746792-G-A
• rs17083008
• XR_007059337.1:n.2375G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

MYCT1 (HGNC:23172): (MYC target 1) Predicted to act upstream of or within hematopoietic stem cell homeostasis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYCT1	XR_007059337.1	n.2375G>A		non_coding_transcript_exon_variant	Exon 5 of 5
MYCT1	XR_007059338.1	n.2137G>A		non_coding_transcript_exon_variant	Exon 4 of 4
MYCT1	XR_007059339.1	n.2217G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.542 AC: 22442 AN: 41436

American (AMR) AF: 0.195 AC: 2982 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3466

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4820

European-Finnish (FIN) AF: 0.189 AC: 1989 AN: 10550

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12277 AN: 67978

Other (OTH) AF: 0.283 AC: 595 AN: 2106

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17083008; hg19: chr6-153067927;