1-212472676-C-T

Variant names:

• chr1-212472676-C-T
• rs6694514
• ENST00000850337.1:n.204G>A

Variant summary

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

The NR_183725.1(LINC02771):​n.202+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,112 control chromosomes in the GnomAD database, including 21,523 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 0.49 (21523 hom., cov: 32)
• Consequence: LINC02771 NR_183725.1 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 4 publications found

Genes affected

LINC02771 (HGNC:54291): (long intergenic non-protein coding RNA 2771)

LINC01740 (HGNC:52528): (long intergenic non-protein coding RNA 1740)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183725.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02771	NR_183725.1		n.202+1G>A		splice_donor intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02771	ENST00000850337.1		n.204G>A		non_coding_transcript_exon	Exon 1 of 3
	LINC01740	ENST00000423842.2	TSL:2	n.799+4315C>T		intron	N/A
	LINC02771	ENST00000661486.1		n.229+1G>A		splice_donor intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75018 AN: 151994 Hom.: 21487 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.494 AC: 75106 AN: 152112 Hom.: 21523 Cov.: 32 AF XY: 0.482 AC XY: 35880 AN XY: 74382

African (AFR) AF: 0.800 AC: 33201 AN: 41490

American (AMR) AF: 0.417 AC: 6364 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.170 AC: 877 AN: 5168

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2939 AN: 10588

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27057 AN: 67994

Other (OTH) AF: 0.477 AC: 1005 AN: 2106

Alfa AF: 0.440 Hom.: 2098

Bravo AF: 0.517

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.5
DANN	Benign	0.48
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6694514; hg19: chr1-212646018;