rs723464

Variant names:

• chr4-132661436-A-G
• rs723464
• ENST00000513270.1:n.324-826A>G

Variant summary

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

The ENST00000513270.1(LINC01256):​n.324-826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,070 control chromosomes in the GnomAD database, including 8,078 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 (8078 hom., cov: 31)
• Consequence: LINC01256 ENST00000513270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01256	NR_126401.1	n.324-826A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01256	ENST00000513270.1	n.324-826A>G		intron_variant	Intron 2 of 3	2
LINC01256	ENST00000667267.1	n.522-826A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48352 AN: 150964 Hom.: 8084 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.320 AC: 48338 AN: 151070 Hom.: 8078 Cov.: 31 AF XY: 0.317 AC XY: 23350 AN XY: 73756

African (AFR) AF: 0.254 AC: 10493 AN: 41326

American (AMR) AF: 0.265 AC: 4030 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3462

East Asian (EAS) AF: 0.134 AC: 690 AN: 5166

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4810

European-Finnish (FIN) AF: 0.338 AC: 3450 AN: 10212

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.376 AC: 25423 AN: 67616

Other (OTH) AF: 0.365 AC: 766 AN: 2098

Alfa AF: 0.345 Hom.: 1198

Bravo AF: 0.312

Asia WGS AF: 0.249 AC: 856 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.79
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs723464; hg19: chr4-133582591;