chr4-132641763-C-T

Variant names:

• chr4-132641763-C-T
• rs725304
• ENST00000667267.1:n.327C>T

Variant summary

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

The ENST00000667267.1(LINC01256):​n.327C>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 0.317 in 151,720 control chromosomes in the GnomAD database, including 8,098 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 (8098 hom., cov: 31)
• Consequence: LINC01256 ENST00000667267.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667267.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01256	NR_126401.1		n.189-2945C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01256	ENST00000667267.1		n.327C>T		non_coding_transcript_exon	Exon 3 of 6
	LINC01256	ENST00000513270.1	TSL:2	n.189-2945C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48046 AN: 151602 Hom.: 8103 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.317 AC: 48031 AN: 151720 Hom.: 8098 Cov.: 31 AF XY: 0.313 AC XY: 23212 AN XY: 74116

African (AFR) AF: 0.227 AC: 9389 AN: 41350

American (AMR) AF: 0.266 AC: 4051 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.161 AC: 829 AN: 5158

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3614 AN: 10492

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25898 AN: 67886

Other (OTH) AF: 0.358 AC: 753 AN: 2106

Alfa AF: 0.207 Hom.: 487

Bravo AF: 0.307

Asia WGS AF: 0.253 AC: 878 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.64
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs725304; hg19: chr4-133562918;