rs633596

chr6-152744352-A-Gchr6-152744352-A-T

Variant summary

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

The XR_007059337.1(MYCT1):n.1153-1218A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,094 control chromosomes in the GnomAD database, including 7,510 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 0.26 (7510 hom., cov: 32)
• Consequence: MYCT1 XR_007059337.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

MYCT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYCT1	XR_007059337.1	n.1153-1218A>G		intron_variant, non_coding_transcript_variant
MYCT1	XR_007059338.1	n.915-1218A>G		intron_variant, non_coding_transcript_variant
MYCT1	XR_007059339.1	n.995-1218A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39995 AN: 151976 Hom.: 7469 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.264 AC: 40089 AN: 152094 Hom.: 7510 Cov.: 32 AF XY: 0.262 AC XY: 19451 AN XY: 74356

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.247

Alfa AF: 0.164 Hom.: 1435

Bravo AF: 0.277

Asia WGS AF: 0.227 AC: 786 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.51
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs633596; hg19: chr6-153065487;