rs11812623

Variant names:

• chr10-78427948-G-A
• rs11812623
• ENST00000421324.4:n.51-100803G>A

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-100803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,156 control chromosomes in the GnomAD database, including 1,010 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 0.099 (1010 hom., cov: 32)
• Consequence: ENSG00000282863 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

ENSG00000282863 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 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
ENSG00000282863	ENST00000421324.4	n.51-100803G>A		intron_variant	Intron 1 of 2	1
ENSG00000282863	ENST00000510550.2	n.156+21249G>A		intron_variant	Intron 1 of 3	4
LINC00595	ENST00000624665.3	n.332-97382G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15140 AN: 152038 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0995 AC: 15139 AN: 152156 Hom.: 1010 Cov.: 32 AF XY: 0.0971 AC XY: 7219 AN XY: 74372

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.107

Alfa AF: 0.124 Hom.: 759

Bravo AF: 0.100

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11812623; hg19: chr10-80187705;