rs12763437

Variant names:

• chr10-78453560-G-A
• rs12763437
• ENST00000421324.4:n.51-75191G>A

Variant summary

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

The ENST00000421324.4(LINC00856):​n.51-75191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,140 control chromosomes in the GnomAD database, including 446 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 0.072 (446 hom., cov: 32)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 2 publications found

Genes affected

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

LOC107984245 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 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.51-75191G>A		intron	N/A
	LINC00856	ENST00000510550.2	TSL:4	n.156+46861G>A		intron	N/A
	LINC00856	ENST00000624665.3	TSL:2	n.332-71770G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10889 AN: 152022 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0716 AC: 10892 AN: 152140 Hom.: 446 Cov.: 32 AF XY: 0.0696 AC XY: 5172 AN XY: 74360

African (AFR) AF: 0.0544 AC: 2258 AN: 41508

American (AMR) AF: 0.0661 AC: 1011 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0439 AC: 211 AN: 4810

European-Finnish (FIN) AF: 0.0754 AC: 798 AN: 10578

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6095 AN: 67996

Other (OTH) AF: 0.0812 AC: 171 AN: 2106

Alfa AF: 0.0717 Hom.: 58

Bravo AF: 0.0701

Asia WGS AF: 0.0530 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.22
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12763437; hg19: chr10-80213317;