rs1149732

Variant names:

• chr10-78226595-C-T
• rs1149732
• ENST00000634389.1:n.407+12580C>T

Variant summary

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

The ENST00000634389.1(LINC00856):​n.407+12580C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,148 control chromosomes in the GnomAD database, including 6,966 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 0.28 (6966 hom., cov: 33)
• Consequence: LINC00856 ENST00000634389.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 1 publications found

Genes affected

LINC00856 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 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
LINC00856	ENST00000634389.1	n.407+12580C>T		intron_variant	Intron 3 of 3	4
LINC00856	ENST00000634930.2	n.73+47349C>T		intron_variant	Intron 1 of 4	3
LINC00856	ENST00000634946.1	n.55+47349C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42061 AN: 152028 Hom.: 6964 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.276 AC: 42064 AN: 152148 Hom.: 6966 Cov.: 33 AF XY: 0.277 AC XY: 20624 AN XY: 74350

African (AFR) AF: 0.102 AC: 4227 AN: 41546

American (AMR) AF: 0.383 AC: 5855 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3468

East Asian (EAS) AF: 0.125 AC: 646 AN: 5182

South Asian (SAS) AF: 0.246 AC: 1188 AN: 4826

European-Finnish (FIN) AF: 0.390 AC: 4104 AN: 10536

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24089 AN: 67978

Other (OTH) AF: 0.277 AC: 585 AN: 2114

Alfa AF: 0.334 Hom.: 4748

Bravo AF: 0.269

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1149732; hg19: chr10-79986352;