rs2486007

Variant names:

• chr1-43968941-A-G
• rs2486007
• ENST00000647729.2:n.1465T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647729.2(ENSG00000285649):​n.1465T>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 ENST00000647729.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 2 publications found

Genes affected

ENSG00000285649 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647729.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285649	ENST00000647729.2		n.1465T>C		non_coding_transcript_exon	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

African (AFR) AF: 0.162 AC: 6706 AN: 41464

American (AMR) AF: 0.177 AC: 2703 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3470

East Asian (EAS) AF: 0.0950 AC: 492 AN: 5180

South Asian (SAS) AF: 0.196 AC: 946 AN: 4818

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10596

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6855 AN: 67984

Other (OTH) AF: 0.122 AC: 256 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2486007;

hg19: chr1-44434613;