rs634125

Positions:

• chr1-60069421-G-A
• chr1-60069421-G-C

Variant summary

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

The ENST00000371201.3(C1orf87):​c.107+3116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,898 control chromosomes in the GnomAD database, including 12,230 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 0.39 (12230 hom., cov: 32)
• Consequence: C1orf87 ENST00000371201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66

Genes affected

C1orf87 (HGNC:28547): (chromosome 1 open reading frame 87)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf87	NM_152377.3	c.107+3116C>T		intron_variant		ENST00000371201.3	NP_689590.1
C1orf87	XM_017000308.2	c.107+3116C>T		intron_variant			XP_016855797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf87	ENST00000371201.3	c.107+3116C>T		intron_variant		1	NM_152377.3	ENSP00000360244	P1
C1orf87	ENST00000450089.6	c.107+3116C>T		intron_variant		5		ENSP00000389432

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59592 AN: 151780 Hom.: 12225 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.393 AC: 59625 AN: 151898 Hom.: 12230 Cov.: 32 AF XY: 0.397 AC XY: 29492 AN XY: 74216

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.394

Alfa AF: 0.413 Hom.: 2228

Bravo AF: 0.369

Asia WGS AF: 0.442 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.24

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: rs634125; hg19: chr1-60535093;