1-162378872-C-T

Variant names:

• chr1-162378872-C-T
• rs164188
• ENST00000420220.1:c.-11-3019C>T

Variant summary

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

The ENST00000420220.1(ENSG00000254706):​c.-11-3019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,300,418 control chromosomes in the GnomAD database, including 649,096 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 1.0 (75506 hom., cov: 31)
  • Exomes 𝑓: 1.0 (573590 hom.)
• Consequence: ENSG00000254706 ENST00000420220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 6 publications found

Genes affected

ENSG00000254706 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420220.1. 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_001135240.4		c.-171C>T		upstream_gene	N/A	NP_001128712.2	A1L170-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254706	ENST00000420220.1	TSL:5	c.-11-3019C>T		intron	N/A	ENSP00000398035.1	F8W6W0
	C1orf226	ENST00000426197.2	TSL:2	c.-42C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 3	ENSP00000413150.2	A1L170-2
	C1orf226	ENST00000426197.2	TSL:2	c.-42C>T		5_prime_UTR	Exon 1 of 3	ENSP00000413150.2	A1L170-2

Frequencies

GnomAD3 genomes AF: 0.996 AC: 151525 AN: 152162 Hom.: 75448 Cov.: 31

Gnomad AFR AF: 0.985

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.999

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.999

GnomAD2 exomes AF: 0.999 AC: 149519 AN: 149656 AF XY: 0.999

Gnomad AFR exome AF: 0.984

Gnomad AMR exome AF: 1.00

Gnomad ASJ exome AF: 1.00

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 1.00

GnomAD4 exome AF: 1.00 AC: 1147658 AN: 1148138 Hom.: 573590 Cov.: 14 AF XY: 1.00 AC XY: 572819 AN XY: 573012

African (AFR) AF: 0.986 AC: 26249 AN: 26614

American (AMR) AF: 0.999 AC: 34810 AN: 34828

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 23164 AN: 23164

East Asian (EAS) AF: 1.00 AC: 33944 AN: 33944

South Asian (SAS) AF: 1.00 AC: 73187 AN: 73188

European-Finnish (FIN) AF: 1.00 AC: 48686 AN: 48686

Middle Eastern (MID) AF: 1.00 AC: 3633 AN: 3634

European-Non Finnish (NFE) AF: 1.00 AC: 854714 AN: 854776

Other (OTH) AF: 0.999 AC: 49271 AN: 49304

GnomAD4 genome AF: 0.996 AC: 151642 AN: 152280 Hom.: 75506 Cov.: 31 AF XY: 0.996 AC XY: 74148 AN XY: 74446

African (AFR) AF: 0.985 AC: 40940 AN: 41560

American (AMR) AF: 0.999 AC: 15285 AN: 15298

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5154 AN: 5154

South Asian (SAS) AF: 1.00 AC: 4818 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68034 AN: 68036

Other (OTH) AF: 0.999 AC: 2111 AN: 2114

Alfa AF: 0.998 Hom.: 13701

Bravo AF: 0.995

Asia WGS AF: 1.00 AC: 3477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.71
PhyloP100		-1.6
PromoterAI		-0.0026	Neutral
Mutation Taster		=300/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs164188;

hg19: chr1-162348662;