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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984245	XR_001747513.2	n.3858+4360C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00856	ENST00000421324.4	n.51-75191G>A		intron_variant	Intron 1 of 2	1
LINC00856	ENST00000510550.2	n.156+46861G>A		intron_variant	Intron 1 of 3	4
LINC00856	ENST00000624665.3	n.332-71770G>A		intron_variant	Intron 1 of 3	2

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 v4.3

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;