ENST00000638644.1:n.32-2389A>G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01226	ENST00000638644.1	n.32-2389A>G		intron_variant	Intron 1 of 4	4
LINC01226	ENST00000639741.1	n.127-2386A>G		intron_variant	Intron 1 of 2	4
LINC01226	ENST00000639839.1	n.237-2386A>G		intron_variant	Intron 2 of 4	4
LINC01226	ENST00000640226.1	n.133-2389A>G		intron_variant	Intron 1 of 3	4

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

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.595

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4949425; hg19: chr1-31999484;