rs10857810

Positions:

• chr1-110059175-C-G
• chr1-110059175-C-T

Variant summary

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

The ENST00000554749.1(ENSG00000258634):​n.836C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,174 control chromosomes in the GnomAD database, including 3,874 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 0.21 (3874 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: ENSG00000258634 ENST00000554749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

Genes affected

ENSG00000258634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.110059175C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258634	ENST00000554749.1	n.836C>G		non_coding_transcript_exon_variant	1/1	6
STRIP1	ENST00000473429.5	n.4213+4373C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32058 AN: 151994 Hom.: 3870 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.145 AC: 9 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.146 AC XY: 7 AN XY: 48

Gnomad4 AFR exome AF: 0.375

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.0833

GnomAD4 genome AF: 0.211 AC: 32084 AN: 152112 Hom.: 3874 Cov.: 32 AF XY: 0.216 AC XY: 16057 AN XY: 74354

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.220

Alfa AF: 0.211 Hom.: 481

Bravo AF: 0.211

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857810; hg19: chr1-110601797; COSMIC: COSV63928644;