1-154565729-C-T

Variant names:

• chr1-154565729-C-T
• rs4845652
• ENST00000659429.2:n.651G>A

Variant summary

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

The ENST00000659429.2(ENSG00000286391):​n.651G>A 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 0.102 in 152,234 control chromosomes in the GnomAD database, including 889 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 0.10 (889 hom., cov: 32)
• Consequence: ENSG00000286391 ENST00000659429.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 25 publications found

Genes affected

ENSG00000286391 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659429.2. 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
	ENSG00000286391	ENST00000659429.2		n.651G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286391	ENST00000664303.3		n.795G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286391	ENST00000666466.3		n.686G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15455 AN: 152116 Hom.: 887 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.102 AC: 15468 AN: 152234 Hom.: 889 Cov.: 32 AF XY: 0.101 AC XY: 7547 AN XY: 74448

African (AFR) AF: 0.129 AC: 5363 AN: 41530

American (AMR) AF: 0.112 AC: 1707 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.118 AC: 614 AN: 5182

South Asian (SAS) AF: 0.150 AC: 724 AN: 4828

European-Finnish (FIN) AF: 0.0553 AC: 587 AN: 10606

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0830 AC: 5646 AN: 68006

Other (OTH) AF: 0.118 AC: 249 AN: 2112

Alfa AF: 0.0876 Hom.: 1313

Bravo AF: 0.105

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.32
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4845652; hg19: chr1-154538205;