NM_001085375.2:c.318-153A>G

Variant names:

• chr1-162383029-A-G
• rs1123005
• NM_001085375.2:c.318-153A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001085375.2(C1orf226):​c.318-153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,160 control chromosomes in the GnomAD database, including 2,854 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 0.18 (2854 hom., cov: 33)
• Consequence: C1orf226 NM_001085375.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 2 publications found

Genes affected

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

ENSG00000254706 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085375.2. 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
	C1orf226	NM_001085375.2	MANE Select	c.318-153A>G		intron	N/A	NP_001078844.1
	C1orf226	NM_001135240.4		c.318-153A>G		intron	N/A	NP_001128712.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf226	ENST00000458626.4	TSL:1 MANE Select	c.318-153A>G		intron	N/A	ENSP00000437071.1
	ENSG00000254706	ENST00000420220.1	TSL:5	c.318-153A>G		intron	N/A	ENSP00000398035.1
	C1orf226	ENST00000426197.2	TSL:2	c.447-153A>G		intron	N/A	ENSP00000413150.2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27557 AN: 152042 Hom.: 2848 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.181 AC: 27602 AN: 152160 Hom.: 2854 Cov.: 33 AF XY: 0.184 AC XY: 13699 AN XY: 74394

African (AFR) AF: 0.257 AC: 10662 AN: 41484

American (AMR) AF: 0.219 AC: 3347 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1740 AN: 5164

South Asian (SAS) AF: 0.140 AC: 674 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1461 AN: 10600

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8681 AN: 68008

Other (OTH) AF: 0.176 AC: 373 AN: 2116

Alfa AF: 0.161 Hom.: 473

Bravo AF: 0.193

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.52
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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: rs1123005; hg19: chr1-162352819;