1-162378847-C-T

Variant names:

• chr1-162378847-C-T
• rs164187
• ENST00000420220.1:c.-11-3044C>T

Variant summary

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

The ENST00000420220.1(ENSG00000254706):​c.-11-3044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 954,828 control chromosomes in the GnomAD database, including 13,297 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 0.15 (1790 hom., cov: 32)
  • Exomes 𝑓: 0.16 (11507 hom.)
• Consequence: ENSG00000254706 ENST00000420220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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.-196C>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.-11-3044C>T		intron	N/A	ENSP00000398035.1	F8W6W0
	C1orf226	ENST00000426197.2	TSL:2	c.-67C>T		5_prime_UTR	Exon 1 of 3	ENSP00000413150.2	A1L170-2
	ENSG00000254706	ENST00000431696.1	TSL:4	c.227-3044C>T		intron	N/A	ENSP00000405676.2	H7C2G1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22336 AN: 152032 Hom.: 1787 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.164 AC: 131384 AN: 802678 Hom.: 11507 Cov.: 10 AF XY: 0.164 AC XY: 66423 AN XY: 405564

African (AFR) AF: 0.0910 AC: 1712 AN: 18804

American (AMR) AF: 0.113 AC: 2711 AN: 24030

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 4417 AN: 17666

East Asian (EAS) AF: 0.0932 AC: 2814 AN: 30182

South Asian (SAS) AF: 0.144 AC: 7670 AN: 53296

European-Finnish (FIN) AF: 0.171 AC: 7701 AN: 44950

Middle Eastern (MID) AF: 0.303 AC: 796 AN: 2630

European-Non Finnish (NFE) AF: 0.169 AC: 97298 AN: 574762

Other (OTH) AF: 0.172 AC: 6265 AN: 36358

GnomAD4 genome AF: 0.147 AC: 22346 AN: 152150 Hom.: 1790 Cov.: 32 AF XY: 0.146 AC XY: 10852 AN XY: 74360

African (AFR) AF: 0.0879 AC: 3648 AN: 41520

American (AMR) AF: 0.137 AC: 2093 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3470

East Asian (EAS) AF: 0.0633 AC: 327 AN: 5162

South Asian (SAS) AF: 0.144 AC: 692 AN: 4812

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10592

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12226 AN: 67984

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.170 Hom.: 3889

Bravo AF: 0.140

Asia WGS AF: 0.120 AC: 415 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	1.6
DANN	Benign	0.79
PhyloP100		-0.49
PromoterAI		-0.0060	Neutral
Mutation Taster		=299/1	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: rs164187; hg19: chr1-162348637; COSMIC: COSV63397054; COSMIC: COSV63397054;