rs644921

Variant names:

• chr20-12941840-T-G
• rs644921
• ENST00000456265.1:n.892-904A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000456265.1(LINC01722):​n.892-904A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 129,758 control chromosomes in the GnomAD database, including 80 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 0.026 (80 hom., cov: 22)
• Consequence: LINC01722 ENST00000456265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 0 publications found

Genes affected

LINC01722 (HGNC:52510): (long intergenic non-protein coding RNA 1722)

LINC01723 (HGNC:52511): (long intergenic non-protein coding RNA 1723)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0257 (3331/129758) while in subpopulation NFE AF = 0.0452 (2650/58666). AF 95% confidence interval is 0.0437. There are 80 homozygotes in GnomAd4. There are 1449 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 80 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01722	NR_109868.1	n.892-904A>C		intron_variant	Intron 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01722	ENST00000456265.1	n.892-904A>C		intron_variant	Intron 3 of 11	1
LINC01723	ENST00000716720.1	n.787+3651T>G		intron_variant	Intron 4 of 4
LINC01723	ENST00000716721.1	n.692+3651T>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3330 AN: 129686 Hom.: 80 Cov.: 22

Gnomad AFR AF: 0.00597

Gnomad AMI AF: 0.00121

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.0215

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.00362

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0184

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

GnomAD4 genome AF: 0.0257 AC: 3331 AN: 129758 Hom.: 80 Cov.: 22 AF XY: 0.0232 AC XY: 1449 AN XY: 62574

African (AFR) AF: 0.00595 AC: 217 AN: 36440

American (AMR) AF: 0.0106 AC: 134 AN: 12596

Ashkenazi Jewish (ASJ) AF: 0.0215 AC: 67 AN: 3114

East Asian (EAS) AF: 0.00 AC: 0 AN: 4670

South Asian (SAS) AF: 0.0220 AC: 86 AN: 3904

European-Finnish (FIN) AF: 0.0190 AC: 144 AN: 7584

Middle Eastern (MID) AF: 0.00391 AC: 1 AN: 256

European-Non Finnish (NFE) AF: 0.0452 AC: 2650 AN: 58666

Other (OTH) AF: 0.0182 AC: 31 AN: 1702

Alfa AF: 0.0416 Hom.: 10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.46
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs644921; hg19: chr20-12922488;