1-231528457-G-C

Position:

• chr1-231528457-G-C

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.-323C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 450,060 control chromosomes in the GnomAD database, including 43,466 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 0.48 (19308 hom., cov: 33)
  • Exomes 𝑓: 0.39 (24158 hom.)
• Consequence: ENSG00000287856 ENST00000662216.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

Genes affected

ENSG00000287856 (HGNC:):

ENSG00000233461 (HGNC:58098):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC122526782	NR_173106.1	n.100C>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287856	ENST00000662216.1	c.-323C>G		5_prime_UTR_variant	1/7			ENSP00000499467.1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72760 AN: 152026 Hom.: 19253 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.392 AC: 116743 AN: 297916 Hom.: 24158 Cov.: 0 AF XY: 0.392 AC XY: 60138 AN XY: 153574

Gnomad4 AFR exome AF: 0.708

Gnomad4 AMR exome AF: 0.516

Gnomad4 ASJ exome AF: 0.351

Gnomad4 EAS exome AF: 0.553

Gnomad4 SAS exome AF: 0.412

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.410

GnomAD4 genome AF: 0.479 AC: 72880 AN: 152144 Hom.: 19308 Cov.: 33 AF XY: 0.472 AC XY: 35141 AN XY: 74374

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.463

Alfa AF: 0.251 Hom.: 534

Bravo AF: 0.508

Asia WGS AF: 0.500 AC: 1741 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	0.22
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1630250; hg19: chr1-231664203;