rs2486007

Variant names:

• chr1-43968941-A-G
• rs2486007
• ENST00000647729.1:n.1454T>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285649	ENST00000647729.1	n.1454T>C		non_coding_transcript_exon_variant	Exon 4 of 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;