1-162383151-G-C

Variant names:

• chr1-162383151-G-C
• rs11806859
• NM_001085375.2:c.318-31G>C

Variant summary

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

The NM_001085375.2(C1orf226):​c.318-31G>C 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. There are indicators that this mutation may affect the branch point..

• Frequency: Genomes: not found (cov: 33)
• Consequence: C1orf226 NM_001085375.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

C1orf226 (HGNC:34351): (chromosome 1 open reading frame 226)

ENSG00000254706 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: This position, referring to a specific DNA site, is a probable branch point but rather VUS (scored 4 / 10). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf226	NM_001085375.2	c.318-31G>C		intron_variant	Intron 1 of 1	ENST00000458626.4	NP_001078844.1
C1orf226	NM_001135240.3	c.447-31G>C		intron_variant	Intron 2 of 2		NP_001128712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf226	ENST00000458626.4	c.318-31G>C		intron_variant	Intron 1 of 1	1	NM_001085375.2	ENSP00000437071.1
ENSG00000254706	ENST00000420220.1	c.318-31G>C		intron_variant	Intron 3 of 3	5		ENSP00000398035.1
C1orf226	ENST00000426197.2	c.447-31G>C		intron_variant	Intron 2 of 2	2		ENSP00000413150.2
ENSG00000254706	ENST00000367932.3	n.*325-31G>C		intron_variant	Intron 2 of 2	4		ENSP00000356909.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.61
DANN	Benign	0.69
BranchPoint Hunter		4.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs11806859; hg19: chr1-162352941;