rs2486007

Positions:

• chr1-43968941-A-G

Variant summary

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

The ENST00000647729.1(ENSG00000285649):​n.1454T>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 0.129 in 152,102 control chromosomes in the GnomAD database, including 1,408 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 0.13 (1408 hom., cov: 32)
• Consequence: ENSG00000285649 ENST00000647729.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

ENSG00000285649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 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
ENSG00000285649	ENST00000647729.1	n.1454T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19607 AN: 151984 Hom.: 1408 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.129 AC: 19616 AN: 152102 Hom.: 1408 Cov.: 32 AF XY: 0.130 AC XY: 9688 AN XY: 74364

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.122

Alfa AF: 0.117 Hom.: 159

Bravo AF: 0.137

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
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: rs2486007; hg19: chr1-44434613;