chr2-129936499-A-C

Variant names:

• chr2-129936499-A-C
• rs6760544
• ENST00000450840.1:n.346+2988A>C

Variant summary

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

The ENST00000450840.1(LINC01856):​n.346+2988A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,822 control chromosomes in the GnomAD database, including 28,545 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 0.59 (28545 hom., cov: 31)
• Consequence: LINC01856 ENST00000450840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 11 publications found

Genes affected

LINC01856 (HGNC:52672): (long intergenic non-protein coding RNA 1856)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01856	NR_110285.1	n.346+2988A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01856	ENST00000450840.1	n.346+2988A>C		intron_variant	Intron 3 of 3	2
LINC01856	ENST00000769638.1	n.183+2988A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89687 AN: 151704 Hom.: 28555 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.591 AC: 89689 AN: 151822 Hom.: 28545 Cov.: 31 AF XY: 0.586 AC XY: 43488 AN XY: 74172

African (AFR) AF: 0.333 AC: 13782 AN: 41332

American (AMR) AF: 0.690 AC: 10534 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2340 AN: 3464

East Asian (EAS) AF: 0.659 AC: 3388 AN: 5144

South Asian (SAS) AF: 0.652 AC: 3134 AN: 4810

European-Finnish (FIN) AF: 0.566 AC: 5963 AN: 10534

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48368 AN: 67954

Other (OTH) AF: 0.611 AC: 1288 AN: 2108

Alfa AF: 0.644 Hom.: 12106

Bravo AF: 0.587

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.093
DANN	Benign	0.18
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6760544; hg19: chr2-130694072;