chr20-12941840-T-G

Position:

• chr20-12941840-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 80 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01722	NR_109868.1	n.892-904A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01722	ENST00000456265.1	n.892-904A>C		intron_variant		1

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

Gnomad4 AFR AF: 0.00595

Gnomad4 AMR AF: 0.0106

Gnomad4 ASJ AF: 0.0215

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0190

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0182

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs644921; hg19: chr20-12922488;