1-234758255-G-T

Variant names:

• chr1-234758255-G-T
• rs17829302
• ENST00000624397.1:n.1802C>A

Variant summary

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

The NR_148962.1(LINC02961):​n.1802C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0676 in 152,372 control chromosomes in the GnomAD database, including 438 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 0.068 (438 hom., cov: 31)
  • Exomes 𝑓: 0.047 (0 hom.)
• Consequence: LINC02961 NR_148962.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 1 publications found

Genes affected

LINC02961 (HGNC:55986): (long intergenic non-protein coding RNA 2961)

ENSG00000289377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_148962.1. 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
	LINC02961	NR_148962.1		n.1802C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02961	ENST00000624397.1	TSL:6	n.1802C>A		non_coding_transcript_exon	Exon 1 of 1
	LINC02961	ENST00000640945.1	TSL:6	n.1802C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289377	ENST00000771897.1		n.677-5220C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10285 AN: 152062 Hom.: 439 Cov.: 31

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.0672

GnomAD4 exome AF: 0.0469 AC: 9 AN: 192 Hom.: 0 Cov.: 0 AF XY: 0.0673 AC XY: 7 AN XY: 104

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0500 AC: 5 AN: 100

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0263 AC: 2 AN: 76

Other (OTH) AF: 0.200 AC: 2 AN: 10

GnomAD4 genome AF: 0.0676 AC: 10287 AN: 152180 Hom.: 438 Cov.: 31 AF XY: 0.0675 AC XY: 5020 AN XY: 74402

African (AFR) AF: 0.0170 AC: 706 AN: 41512

American (AMR) AF: 0.0904 AC: 1383 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.112 AC: 537 AN: 4802

European-Finnish (FIN) AF: 0.0666 AC: 706 AN: 10602

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6409 AN: 68004

Other (OTH) AF: 0.0660 AC: 139 AN: 2106

Alfa AF: 0.0777 Hom.: 985

Bravo AF: 0.0656

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs17829302; hg19: chr1-234894002;