rs11812623

Variant names:

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

Variant summary

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

The ENST00000421324.4(LINC00856):​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: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421324.4. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00856	ENST00000421324.4	TSL:1	n.51-100803G>A		intron	N/A
	LINC00856	ENST00000510550.2	TSL:4	n.156+21249G>A		intron	N/A
	LINC00856	ENST00000624665.3	TSL:2	n.332-97382G>A		intron	N/A

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

African (AFR) AF: 0.0273 AC: 1136 AN: 41540

American (AMR) AF: 0.148 AC: 2270 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 311 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.0765 AC: 368 AN: 4812

European-Finnish (FIN) AF: 0.126 AC: 1336 AN: 10570

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9368 AN: 67982

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.121 Hom.: 1019

Bravo AF: 0.100

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.31
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11812623; hg19: chr10-80187705;