rs3908399

Variant names:

• chr20-12920627-G-A
• rs3908399
• ENST00000456265.1:n.1279+2C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-12920627-G-A
• chr20-12920627-G-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The ENST00000456265.1(LINC01722):​n.1279+2C>T variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,092 control chromosomes in the GnomAD database, including 3,508 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 0.20 (3508 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01722 ENST00000456265.1 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene. Cryptic splice site detected, with MaxEntScore 11, offset of 0 (no position change), new splice context is: aagGTaagt. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456265.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01722	NR_109868.1		n.1279+2C>T		splice_donor intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01722	ENST00000456265.1	TSL:1	n.1279+2C>T		splice_donor intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29927 AN: 151974 Hom.: 3507 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.215

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.197 AC: 29932 AN: 152092 Hom.: 3508 Cov.: 32 AF XY: 0.202 AC XY: 15038 AN XY: 74350

African (AFR) AF: 0.0718 AC: 2981 AN: 41516

American (AMR) AF: 0.270 AC: 4124 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.153 AC: 790 AN: 5176

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2939 AN: 10548

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16228 AN: 67964

Other (OTH) AF: 0.217 AC: 457 AN: 2108

Alfa AF: 0.234 Hom.: 2702

Bravo AF: 0.193

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.84
PhyloP100		-0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3908399;

hg19: chr20-12901275;