rs2060700

Positions:

• chr1-106081185-A-G

Variant summary

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

The ENST00000429608.1(ENSG00000237480):​n.25A>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 0.138 in 1,558,114 control chromosomes in the GnomAD database, including 18,335 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 0.17 (2636 hom., cov: 32)
  • Exomes 𝑓: 0.13 (15699 hom.)
• Consequence: ENSG00000237480 ENST00000429608.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885

Genes affected

ENSG00000230932 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC126987		n.106081185A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230932	ENST00000415580.2	n.195T>C		non_coding_transcript_exon_variant	1/1	6
ENSG00000237480	ENST00000429608.1	n.25A>G		non_coding_transcript_exon_variant	1/2	3
ENSG00000237480	ENST00000655639.1	n.61A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26221 AN: 152060 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.134 AC: 188871 AN: 1405936 Hom.: 15699 Cov.: 29 AF XY: 0.135 AC XY: 93945 AN XY: 696554

Gnomad4 AFR exome AF: 0.239

Gnomad4 AMR exome AF: 0.291

Gnomad4 ASJ exome AF: 0.105

Gnomad4 EAS exome AF: 0.421

Gnomad4 SAS exome AF: 0.172

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.113

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.173 AC: 26282 AN: 152178 Hom.: 2636 Cov.: 32 AF XY: 0.175 AC XY: 13034 AN XY: 74392

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.153

Alfa AF: 0.158 Hom.: 299

Bravo AF: 0.186

Asia WGS AF: 0.259 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060700; hg19: chr1-106623807;