rs3738505

Positions:

• chr1-42767206-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.235 in 1,346,988 control chromosomes in the GnomAD database, including 39,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.23 (4269 hom., cov: 34)
  • Exomes 𝑓: 0.24 (35198 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.18

Genes affected

(HGNC:):

C1orf50 (HGNC:28795): (chromosome 1 open reading frame 50) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 1-42767206-A-T is Benign according to our data. Variant chr1-42767206-A-T is described in ClinVar as [Benign]. Clinvar id is 1235692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42767206A>T		intergenic_region
C1orf50	NM_024097.4	c.-106A>T		upstream_gene_variant		ENST00000372525.7	NP_077002.2
C1orf50	NR_040733.2	n.-43A>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf50	ENST00000372525.7	c.-106A>T		upstream_gene_variant		1	NM_024097.4	ENSP00000361603.4
C1orf50	ENST00000693399.1	n.-39A>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34656 AN: 152160 Hom.: 4266 Cov.: 34

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.236 AC: 282303 AN: 1194710 Hom.: 35198 Cov.: 19 AF XY: 0.241 AC XY: 141327 AN XY: 586650

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.154

Gnomad4 ASJ exome AF: 0.248

Gnomad4 EAS exome AF: 0.355

Gnomad4 SAS exome AF: 0.398

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.228 AC: 34667 AN: 152278 Hom.: 4269 Cov.: 34 AF XY: 0.230 AC XY: 17093 AN XY: 74460

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.234

Alfa AF: 0.208 Hom.: 431

Bravo AF: 0.228

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.72
DANN	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3738505; hg19: chr1-43232877;