rs3000802

Variant names:

• chr1-227421203-G-A
• rs3000802
• ENST00000445817.1:n.341-8202G>A

Variant summary

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

The variant allele was found at a frequency of 0.0664 in 151,734 control chromosomes in the GnomAD database, including 564 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 0.066 (564 hom., cov: 31)
• Consequence: NUCKS1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 2 publications found

Genes affected

LINC01641 (HGNC:52428): (long intergenic non-protein coding RNA 1641)

NUCKS1P1 (HGNC:51943): (nuclear casein kinase and cyclin dependent kinase substrate 1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445817.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01641	ENST00000445817.1	TSL:1	n.341-8202G>A		intron	N/A
	LINC01641	ENST00000436377.1	TSL:2	n.121-4553G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10062 AN: 151654 Hom.: 562 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.00771

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0786

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

GnomAD4 genome AF: 0.0664 AC: 10076 AN: 151734 Hom.: 564 Cov.: 31 AF XY: 0.0694 AC XY: 5138 AN XY: 74078

African (AFR) AF: 0.0154 AC: 638 AN: 41364

American (AMR) AF: 0.135 AC: 2058 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1446 AN: 5160

South Asian (SAS) AF: 0.0328 AC: 157 AN: 4782

European-Finnish (FIN) AF: 0.0911 AC: 949 AN: 10422

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.0653 AC: 4436 AN: 67966

Other (OTH) AF: 0.0780 AC: 164 AN: 2102

Alfa AF: 0.0719 Hom.: 1020

Bravo AF: 0.0734

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.54
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs3000802; hg19: chr1-227608904;