rs6104690

Variant names:

• chr20-11007451-G-A
• rs6104690
• ENST00000378252.3:n.1448+2368G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-11007451-G-A
• chr20-11007451-G-C
• chr20-11007451-G-T

Variant summary

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

The ENST00000378252.3(LINC02871):​n.1448+2368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,948 control chromosomes in the GnomAD database, including 23,860 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 0.56 (23860 hom., cov: 32)
• Consequence: LINC02871 ENST00000378252.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 18 publications found

Genes affected

LINC02871 (HGNC:16180): (long intergenic non-protein coding RNA 2871)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000378252.3. 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
	LINC02871	ENST00000378252.3	TSL:2	n.1448+2368G>A		intron	N/A
	LINC02871	ENST00000603180.6	TSL:4	n.1167+8753G>A		intron	N/A
	LINC02871	ENST00000659767.2		n.1216+8753G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84839 AN: 151830 Hom.: 23848 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.559 AC: 84888 AN: 151948 Hom.: 23860 Cov.: 32 AF XY: 0.555 AC XY: 41198 AN XY: 74262

African (AFR) AF: 0.584 AC: 24211 AN: 41424

American (AMR) AF: 0.520 AC: 7949 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1948 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3267 AN: 5150

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5280 AN: 10542

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38059 AN: 67954

Other (OTH) AF: 0.576 AC: 1215 AN: 2108

Alfa AF: 0.555 Hom.: 99510

Bravo AF: 0.563

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.40

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: rs6104690;

hg19: chr20-10988099;