rs11177982

chr12-69943888-C-Gchr12-69943888-C-T

Variant summary

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

The NM_182530.3(MYRFL):c.2224+7256C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,902 control chromosomes in the GnomAD database, including 1,224 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 0.11 (1224 hom., cov: 27)
• Consequence: MYRFL NM_182530.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

MYRFL (HGNC:26316): (myelin regulatory factor like) Predicted to enable DNA-binding transcription factor activity and sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription, DNA-templated and protein autoprocessing. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PRANCR (HGNC:51126): (progenitor renewal associated non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYRFL	NM_182530.3	c.2224+7256C>G		intron_variant		ENST00000552032.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYRFL	ENST00000552032.7	c.2224+7256C>G		intron_variant		5	NM_182530.3	P2
PRANCR	ENST00000549419.6	n.153-39469G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17407 AN: 151784 Hom.: 1224 Cov.: 27

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.115 AC: 17408 AN: 151902 Hom.: 1224 Cov.: 27 AF XY: 0.114 AC XY: 8480 AN XY: 74232

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.0555

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0580 Hom.: 65

Bravo AF: 0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs11177982; hg19: chr12-70337668;