1-39896394-C-T

Variant names:

• chr1-39896394-C-T
• rs3134615
• NM_001033081.3:c.*978G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001033081.3(MYCL):​c.*978G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MYCL NM_001033081.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 0 publications found

Genes affected

MYCL (HGNC:7555): (MYCL proto-oncogene, bHLH transcription factor) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of inner ear auditory receptor cell differentiation. Located in chromosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYCL-AS1 (HGNC:40386): (MYCL antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033081.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCL	NM_001033081.3	MANE Select	c.*978G>A		3_prime_UTR	Exon 2 of 2	NP_001028253.1	P12524-1
	MYCL	NM_001033082.3		c.*978G>A		3_prime_UTR	Exon 3 of 3	NP_001028254.2	P12524-3
	MYCL-AS1	NR_183424.1		n.273-1349C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCL	ENST00000372816.3	TSL:2 MANE Select	c.*978G>A		3_prime_UTR	Exon 2 of 2	ENSP00000361903.2	P12524-1
	MYCL	ENST00000397332.3	TSL:1	c.*978G>A		3_prime_UTR	Exon 3 of 3	ENSP00000380494.2	P12524-3
	MYCL-AS1	ENST00000418255.2	TSL:2	n.326-1349C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 51112 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 23774

African (AFR) AF: 0.00 AC: 0 AN: 2190

American (AMR) AF: 0.00 AC: 0 AN: 1446

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3216

East Asian (EAS) AF: 0.00 AC: 0 AN: 8242

South Asian (SAS) AF: 0.00 AC: 0 AN: 428

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 82

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 298

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 30988

Other (OTH) AF: 0.00 AC: 0 AN: 4222

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3134615; hg19: chr1-40362066;