Genetic Variant ENSG00000254706:c.-11-3019C>A (chr1-162378872-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

Publications

6 publications found

Variant links:

Genes affected

ENSG00000254706 (HGNC:):

ENSG00000254706 links:

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

C1orf226 links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf226	NM_001135240.4 link	c.-171C>A		upstream_gene_variant			NP_001128712.2	A1L170-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000254706	ENST00000420220.1 link	c.-11-3019C>A	intron_variant	Intron 2 of 3	5	ENSP00000398035.1	F8W6W0
C1orf226	ENST00000426197.2 link	c.-42C>A	5_prime_UTR_variant	Exon 1 of 3	2	ENSP00000413150.2	A1L170-2
ENSG00000254706	ENST00000431696.1 link	c.227-3019C>A	intron_variant	Intron 2 of 2	4	ENSP00000405676.2	H7C2G1
ENSG00000254706	ENST00000367932.3 link	n.153-3019C>A	intron_variant	Intron 1 of 2	4	ENSP00000356909.3	H7BY61

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1148142

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

573014

African (AFR)

AF:

0.00

AC:

AN:

26618

American (AMR)

AF:

0.00

AC:

AN:

34828

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23164

East Asian (EAS)

AF:

0.00

AC:

AN:

33944

South Asian (SAS)

AF:

0.00

AC:

AN:

73188

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48686

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3634

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

854776

Other (OTH)

AF:

0.00

AC:

AN:

49304

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0030

(source)

DANN

Benign

0.59

PhyloP100

-1.6

PromoterAI

-0.0070

Neutral

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over