chr4-86924979-C-A

Variant names:

• chr4-86924979-C-A
• rs2785
• ENST00000473559.5:c.-74+1249G>T

Variant summary

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

The ENST00000473559.5(C4orf36):​c.-74+1249G>T variant causes a intron 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)
• Consequence: C4orf36 ENST00000473559.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 6 publications found

Genes affected

C4orf36 (HGNC:):

AFF1-AS1 (HGNC:53447): (AFF1 antisense RNA 1)

C4orf36 (HGNC:28386): (chromosome 4 open reading frame 36)

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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473559.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFF1-AS1	NR_038841.1		n.1860G>T		non_coding_transcript_exon	Exon 3 of 3
	C4orf36	NM_001414639.1		c.-74+1249G>T		intron	N/A	NP_001401568.1
	C4orf36	NM_001414640.1		c.-143+1249G>T		intron	N/A	NP_001401569.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf36	ENST00000473559.5	TSL:2	c.-74+1249G>T		intron	N/A	ENSP00000420949.1
	ENSG00000284968	ENST00000508280.6	TSL:2	n.1809G>T		non_coding_transcript_exon	Exon 4 of 4
	C4orf36	ENST00000503001.5	TSL:3	n.438+1249G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1023

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-1.0

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: rs2785; hg19: chr4-87846131;