rs16854012

Positions:

• chr1-231227254-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152379.4(C1orf131):​c.511-186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,106 control chromosomes in the GnomAD database, including 857 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 0.089 (857 hom., cov: 31)
• Consequence: C1orf131 NM_152379.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

Genes affected

C1orf131 (HGNC:25332): (chromosome 1 open reading frame 131) Enables RNA binding activity. Located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]

C1orf131 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf131	NM_152379.4	c.511-186T>C		intron_variant		ENST00000366649.7	NP_689592.2
C1orf131	NM_001300830.2	c.508-186T>C		intron_variant			NP_001287759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf131	ENST00000366649.7	c.511-186T>C		intron_variant		1	NM_152379.4	ENSP00000355609.2

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13486 AN: 151988 Hom.: 858 Cov.: 31

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.0936

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0886 AC: 13480 AN: 152106 Hom.: 857 Cov.: 31 AF XY: 0.0944 AC XY: 7018 AN XY: 74346

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0747

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.0955

Alfa AF: 0.0896 Hom.: 1002

Bravo AF: 0.0935

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.46

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

LitVar

Other links and lift over

dbSNP: rs16854012; hg19: chr1-231363000;