rs1984279

Variant names:

• chr20-23332555-A-C
• rs1984279
• ENST00000716734.1:n.138+18775T>G

Variant summary

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

The ENST00000716734.1(NXT1-AS1):​n.138+18775T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,038 control chromosomes in the GnomAD database, including 24,346 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 0.52 (24346 hom., cov: 32)
• Consequence: NXT1-AS1 ENST00000716734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 13 publications found

Genes affected

NXT1-AS1 (HGNC:40734): (NXT1 antisense RNA 1)

LOC105372571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372571	XR_007067746.1	n.3301+12T>G		intron_variant	Intron 1 of 1
LOC105372571	XR_007067747.1	n.3301+12T>G		intron_variant	Intron 1 of 1
LOC105372571	XR_937379.3	n.3301+12T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NXT1-AS1	ENST00000716734.1	n.138+18775T>G		intron_variant	Intron 1 of 1
NXT1-AS1	ENST00000716735.1	n.256+12T>G		intron_variant	Intron 2 of 3
NXT1-AS1	ENST00000716736.1	n.322+12T>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79615 AN: 151920 Hom.: 24289 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.524 AC: 79724 AN: 152038 Hom.: 24346 Cov.: 32 AF XY: 0.526 AC XY: 39053 AN XY: 74308

African (AFR) AF: 0.856 AC: 35497 AN: 41470

American (AMR) AF: 0.468 AC: 7145 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2999 AN: 5162

South Asian (SAS) AF: 0.412 AC: 1981 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4021 AN: 10570

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25056 AN: 67962

Other (OTH) AF: 0.499 AC: 1050 AN: 2106

Alfa AF: 0.421 Hom.: 25125

Bravo AF: 0.551

Asia WGS AF: 0.489 AC: 1702 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	4.5
DANN	Benign	0.68
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1984279; hg19: chr20-23313192;