chr6-152746792-G-A

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;