rs3762318

Variant names:

• chr1-67131436-G-A
• rs3762318
• NM_001276351.2:c.-103-209C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-67131436-G-A
• chr1-67131436-G-C
• chr1-67131436-G-T

Variant summary

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

The NM_001276351.2(C1orf141):​c.-103-209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,994 control chromosomes in the GnomAD database, including 52,539 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 0.83 (52539 hom., cov: 29)
• Consequence: C1orf141 NM_001276351.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf141	NM_001276351.2	c.-103-209C>T		intron_variant	Intron 1 of 7	ENST00000684719.1	NP_001263280.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf141	ENST00000684719.1	c.-103-209C>T		intron_variant	Intron 1 of 7		NM_001276351.2	ENSP00000507487.1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126294 AN: 151876 Hom.: 52509 Cov.: 29

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.831 AC: 126373 AN: 151994 Hom.: 52539 Cov.: 29 AF XY: 0.833 AC XY: 61925 AN XY: 74312

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.805

Alfa AF: 0.834 Hom.: 115707

Bravo AF: 0.828

Asia WGS AF: 0.917 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.19

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: rs3762318; hg19: chr1-67597119;