rs1920122

Variant names:

• chr3-169788353-C-G
• rs1920122
• NM_018657.5:c.*1675C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-169788353-C-G
• chr3-169788353-C-T

Variant summary

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

The NM_018657.5(MYNN):​c.*1675C>G 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: 33)
• Consequence: MYNN NM_018657.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 17 publications found

Genes affected

MYNN (HGNC:14955): (myoneurin) This gene encodes a member of the BTB/POZ and zinc finger domain-containing protein family that are involved in the control of gene expression. Alternative splicing results in multiple transcript variants and a pseudogene has been identified on chromosome 14. [provided by RefSeq, Jun 2010]

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018657.5. 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
	MYNN	NM_018657.5	MANE Select	c.*1675C>G		3_prime_UTR	Exon 8 of 8	NP_061127.1	Q9NPC7-1
	MYNN	NM_001185118.2		c.*1675C>G		3_prime_UTR	Exon 9 of 9	NP_001172047.1	Q9NPC7-1
	MYNN	NM_001185119.1		c.*1675C>G		3_prime_UTR	Exon 6 of 6	NP_001172048.1	Q9NPC7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYNN	ENST00000349841.10	TSL:1 MANE Select	c.*1675C>G		3_prime_UTR	Exon 8 of 8	ENSP00000326240.4	Q9NPC7-1
	MYNN	ENST00000544106.5	TSL:1	c.*1675C>G		3_prime_UTR	Exon 6 of 6	ENSP00000440637.1	Q9NPC7-2
	MYNN	ENST00000900707.1		c.*1675C>G		3_prime_UTR	Exon 9 of 9	ENSP00000570766.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.37
PhyloP100		0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1920122; hg19: chr3-169506141;