1-229224758-T-C

Variant names:

• chr1-229224758-T-C
• rs2988738
• ENST00000430677.1:n.303-808A>G

Variant summary

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

The ENST00000430677.1(ENSG00000233920):​n.303-808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,306 control chromosomes in the GnomAD database, including 251 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 0.039 (251 hom., cov: 32)
• Consequence: ENSG00000233920 ENST00000430677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 2 publications found

Genes affected

ENSG00000233920 (HGNC:):

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430677.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233920	ENST00000430677.1	TSL:3	n.303-808A>G		intron	N/A
	ENSG00000233920	ENST00000651412.1		n.428-808A>G		intron	N/A
	LINC02814	ENST00000716801.1		n.92-26954A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5853 AN: 152188 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0385 AC: 5868 AN: 152306 Hom.: 251 Cov.: 32 AF XY: 0.0420 AC XY: 3125 AN XY: 74486

African (AFR) AF: 0.0303 AC: 1259 AN: 41568

American (AMR) AF: 0.0989 AC: 1511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.198 AC: 1029 AN: 5184

South Asian (SAS) AF: 0.110 AC: 531 AN: 4828

European-Finnish (FIN) AF: 0.0163 AC: 173 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0152 AC: 1036 AN: 68030

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0272 Hom.: 248

Bravo AF: 0.0447

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2988738; hg19: chr1-229360505;