rs1149732

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634930.1(ENSG00000282863):​n.73+47349C>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: ENSG00000282863 ENST00000634930.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

Genes affected

LINC00595 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ENSG00000282863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
LINC00595	ENST00000634389.1	n.407+12580C>T		intron_variant	Intron 3 of 3	4
ENSG00000282863	ENST00000634930.1	n.73+47349C>T		intron_variant	Intron 1 of 3	3
LINC00595	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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.277

Alfa AF: 0.337 Hom.: 4287

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1149732; hg19: chr10-79986352;