rs12134663

Variant names:

• chr1-11778589-A-C
• rs12134663
• NM_001010881.2:c.2340-71A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-11778589-A-C
• chr1-11778589-A-G

Variant summary

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

The NM_001010881.2(C1orf167):​c.2340-71A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,193,464 control chromosomes in the GnomAD database, including 16,231 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 0.12 (1499 hom., cov: 33)
  • Exomes 𝑓: 0.16 (14732 hom.)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 30 publications found

Genes affected

C1orf167 (HGNC:25262): (chromosome 1 open reading frame 167) Implicated in coronary artery disease. [provided by Alliance of Genome Resources, Apr 2022]

C1orf167-AS1 (HGNC:41091): (C1orf167 antisense RNA 1)

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 (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf167	NM_001010881.2	c.2340-71A>C		intron_variant	Intron 10 of 20	ENST00000688073.1	NP_001010881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf167	ENST00000688073.1	c.2340-71A>C		intron_variant	Intron 10 of 20		NM_001010881.2	ENSP00000510540.1
C1orf167-AS1	ENST00000376620.3	n.660+56T>G		intron_variant	Intron 2 of 2	1
C1orf167	ENST00000433342.6	c.1854-71A>C		intron_variant	Intron 10 of 20	5		ENSP00000414909.3
C1orf167	ENST00000312793.9	c.489-71A>C		intron_variant	Intron 3 of 13	2		ENSP00000317749.5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18994 AN: 152092 Hom.: 1503 Cov.: 33

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.164 AC: 170912 AN: 1041254 Hom.: 14732 AF XY: 0.167 AC XY: 83831 AN XY: 501382

African (AFR) AF: 0.0225 AC: 491 AN: 21840

American (AMR) AF: 0.0784 AC: 1612 AN: 20572

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 2571 AN: 11086

East Asian (EAS) AF: 0.102 AC: 1175 AN: 11532

South Asian (SAS) AF: 0.249 AC: 16084 AN: 64484

European-Finnish (FIN) AF: 0.169 AC: 4151 AN: 24494

Middle Eastern (MID) AF: 0.209 AC: 781 AN: 3744

European-Non Finnish (NFE) AF: 0.163 AC: 137954 AN: 846464

Other (OTH) AF: 0.165 AC: 6093 AN: 37038

GnomAD4 genome AF: 0.125 AC: 18989 AN: 152210 Hom.: 1499 Cov.: 33 AF XY: 0.126 AC XY: 9348 AN XY: 74422

African (AFR) AF: 0.0309 AC: 1283 AN: 41574

American (AMR) AF: 0.103 AC: 1574 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3472

East Asian (EAS) AF: 0.103 AC: 532 AN: 5156

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4826

European-Finnish (FIN) AF: 0.168 AC: 1784 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11342 AN: 67988

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.0504 Hom.: 63

Bravo AF: 0.115

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.57
PhyloP100		-0.95
PromoterAI		0.0016	Neutral
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: rs12134663; hg19: chr1-11838646;