1-115271144-C-G

Position:

• chr1-115271144-C-G

Variant summary

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

The ENST00000649888.1(ENSG00000285698):​n.977G>C 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 0.409 in 151,924 control chromosomes in the GnomAD database, including 12,941 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 0.41 (12941 hom., cov: 32)
• Consequence: ENSG00000285698 ENST00000649888.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

ENSG00000285698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285698	ENST00000649888.1	n.977G>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62174 AN: 151806 Hom.: 12936 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.409 AC: 62203 AN: 151924 Hom.: 12941 Cov.: 32 AF XY: 0.413 AC XY: 30662 AN XY: 74272

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.401

Alfa AF: 0.231 Hom.: 459

Bravo AF: 0.415

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057127; hg19: chr1-115813765;