chr1-31533883-A-G

Variant names:

• chr1-31533883-A-G
• rs4949425
• ENST00000638644.1:n.32-2389A>G

Variant summary

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

The ENST00000638644.1(LINC01226):​n.32-2389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,018 control chromosomes in the GnomAD database, including 28,378 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 0.61 (28378 hom., cov: 32)
• Consequence: LINC01226 ENST00000638644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

LINC01226 (HGNC:49678): (long intergenic non-protein coding RNA 1226)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638644.1. 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
	LINC01226	ENST00000638644.1	TSL:4	n.32-2389A>G		intron	N/A
	LINC01226	ENST00000639741.1	TSL:4	n.127-2386A>G		intron	N/A
	LINC01226	ENST00000639839.1	TSL:4	n.237-2386A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92094 AN: 151900 Hom.: 28366 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.606 AC: 92141 AN: 152018 Hom.: 28378 Cov.: 32 AF XY: 0.601 AC XY: 44683 AN XY: 74288

African (AFR) AF: 0.668 AC: 27703 AN: 41462

American (AMR) AF: 0.592 AC: 9035 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1816 AN: 5188

South Asian (SAS) AF: 0.451 AC: 2169 AN: 4812

European-Finnish (FIN) AF: 0.598 AC: 6299 AN: 10530

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41068 AN: 67968

Other (OTH) AF: 0.595 AC: 1256 AN: 2110

Alfa AF: 0.620 Hom.: 3678

Bravo AF: 0.607

Asia WGS AF: 0.412 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4949425; hg19: chr1-31999484;