rs164188

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-162378872-C-A
• chr1-162378872-C-G
• chr1-162378872-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000420220.1(ENSG00000254706):​c.-11-3019C>A 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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>A		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>A		intron	N/A	ENSP00000398035.1	F8W6W0
	C1orf226	ENST00000426197.2	TSL:2	c.-42C>A		5_prime_UTR	Exon 1 of 3	ENSP00000413150.2	A1L170-2
	ENSG00000254706	ENST00000431696.1	TSL:4	c.227-3019C>A		intron	N/A	ENSP00000405676.2	H7C2G1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1148142 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 573014

African (AFR) AF: 0.00 AC: 0 AN: 26618

American (AMR) AF: 0.00 AC: 0 AN: 34828

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23164

East Asian (EAS) AF: 0.00 AC: 0 AN: 33944

South Asian (SAS) AF: 0.00 AC: 0 AN: 73188

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48686

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3634

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 854776

Other (OTH) AF: 0.00 AC: 0 AN: 49304

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0030
DANN	Benign	0.59
PhyloP100		-1.6
PromoterAI		-0.0070	Neutral

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;