chr1-2581777-C-T

Variant names:

• chr1-2581777-C-T
• rs734999
• ENST00000829924.1:n.462C>T

Variant summary

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

The ENST00000829924.1(ENSG00000228037):​n.462C>T 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 0.578 in 152,020 control chromosomes in the GnomAD database, including 26,883 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 0.58 (26881 hom., cov: 32)
  • Exomes 𝑓: 0.42 (2 hom.)
• Consequence: ENSG00000228037 ENST00000829924.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 60 publications found

Genes affected

ENSG00000228037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829924.1. 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
	LOC100996583	NR_121638.1		n.162+127C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228037	ENST00000829924.1		n.462C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228037	ENST00000424215.2	TSL:5	n.945+127C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87682 AN: 151842 Hom.: 26841 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.549

GnomAD4 exome AF: 0.417 AC: 25 AN: 60 Hom.: 2 AF XY: 0.344 AC XY: 11 AN XY: 32

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.389 AC: 7 AN: 18

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.421 AC: 16 AN: 38

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.578 AC: 87774 AN: 151960 Hom.: 26881 Cov.: 32 AF XY: 0.579 AC XY: 42971 AN XY: 74220

African (AFR) AF: 0.795 AC: 32955 AN: 41452

American (AMR) AF: 0.546 AC: 8348 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2784 AN: 5164

South Asian (SAS) AF: 0.659 AC: 3180 AN: 4822

European-Finnish (FIN) AF: 0.500 AC: 5259 AN: 10524

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32103 AN: 67942

Other (OTH) AF: 0.554 AC: 1165 AN: 2104

Alfa AF: 0.503 Hom.: 85725

Bravo AF: 0.584

Asia WGS AF: 0.680 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs734999; hg19: chr1-2513216;