rs2785

Positions:

• chr4-86924979-C-A
• chr4-86924979-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001414639.1(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 NM_001414639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000285458 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C4orf36	NM_001414639.1	c.-74+1249G>T		intron_variant			NP_001401568.1
C4orf36	NM_001414640.1	c.-143+1249G>T		intron_variant			NP_001401569.1
C4orf36	NM_001414641.1	c.-74+1249G>T		intron_variant			NP_001401570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285458	ENST00000473559.5	c.-74+1249G>T		intron_variant		2		ENSP00000420949.1
ENSG00000284968	ENST00000508280.6	n.1809G>T		non_coding_transcript_exon_variant	4/4	2
ENSG00000285458	ENST00000503001.5	n.438+1249G>T		intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs2785; hg19: chr4-87846131;