rs2256432

Variant names:

• chr10-42979175-C-T
• rs2256432
• ENST00000431395.1:n.418-76G>A

Variant summary

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

The ENST00000431395.1(LINC01264):​n.418-76G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,220 control chromosomes in the GnomAD database, including 3,191 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 0.18 (3190 hom., cov: 33)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: LINC01264 ENST00000431395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 2 publications found

Genes affected

LINC01264 (HGNC:50282): (long intergenic non-protein coding RNA 1264)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431395.1. 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
	LINC01264	NR_126352.1		n.418-76G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01264	ENST00000431395.1	TSL:3	n.418-76G>A		intron	N/A
	LINC01264	ENST00000754421.1		n.631-76G>A		intron	N/A
	LINC01264	ENST00000754422.1		n.300-76G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27590 AN: 152088 Hom.: 3190 Cov.: 33

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.143 AC: 2 AN: 14 Hom.: 1 AF XY: 0.200 AC XY: 2 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.181 AC: 27586 AN: 152206 Hom.: 3190 Cov.: 33 AF XY: 0.187 AC XY: 13886 AN XY: 74416

African (AFR) AF: 0.0566 AC: 2353 AN: 41536

American (AMR) AF: 0.303 AC: 4638 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5172

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

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10600

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13868 AN: 67998

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.203 Hom.: 10877

Bravo AF: 0.184

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.58
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2256432; hg19: chr10-43474623;