rs725307

Variant names:

• chr4-132641299-A-G
• rs725307
• ENST00000513270.1:n.189-3409A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-132641299-A-G
• chr4-132641299-A-T

Variant summary

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

The ENST00000513270.1(LINC01256):​n.189-3409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,008 control chromosomes in the GnomAD database, including 8,093 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 0.32 (8093 hom., cov: 32)
• Consequence: LINC01256 ENST00000513270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 3 publications found

Genes affected

LINC01256 (HGNC:49895): (long intergenic non-protein coding RNA 1256)

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 (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513270.1. 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
	LINC01256	NR_126401.1		n.189-3409A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01256	ENST00000513270.1	TSL:2	n.189-3409A>G		intron	N/A
	LINC01256	ENST00000667267.1		n.289-426A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48065 AN: 151890 Hom.: 8098 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.316 AC: 48050 AN: 152008 Hom.: 8093 Cov.: 32 AF XY: 0.313 AC XY: 23242 AN XY: 74326

African (AFR) AF: 0.227 AC: 9392 AN: 41462

American (AMR) AF: 0.266 AC: 4058 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3470

East Asian (EAS) AF: 0.159 AC: 824 AN: 5174

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4808

European-Finnish (FIN) AF: 0.343 AC: 3628 AN: 10582

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25898 AN: 67924

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.279 Hom.: 1406

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.64
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs725307; hg19: chr4-133562454;