ENST00000637807.1:c.2374-6813T>A

Variant names:

• chr7-17444182-T-A
• rs643671
• ENST00000637807.1:c.2374-6813T>A

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2374-6813T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,270 control chromosomes in the GnomAD database, including 66,794 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 0.94 (66794 hom., cov: 31)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• Publications: 1 publications found

Genes affected

ENSG00000283321 (HGNC:):

LINC02888 (HGNC:53765): (long intergenic non-protein coding RNA 2888)

LINC02889 (HGNC:55071): (long intergenic non-protein coding RNA 2889)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02888	NR_110014.1	n.140-4699T>A		intron_variant	Intron 1 of 3
LINC02888	NR_110015.1	n.140-6813T>A		intron_variant	Intron 1 of 2
LOC105375172	XR_001745108.1	n.1895-7949A>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.2374-6813T>A		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142488 AN: 152150 Hom.: 66740 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.937 AC: 142601 AN: 152270 Hom.: 66794 Cov.: 31 AF XY: 0.939 AC XY: 69890 AN XY: 74450

African (AFR) AF: 0.949 AC: 39418 AN: 41542

American (AMR) AF: 0.928 AC: 14189 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3121 AN: 3472

East Asian (EAS) AF: 0.972 AC: 5035 AN: 5182

South Asian (SAS) AF: 0.948 AC: 4579 AN: 4828

European-Finnish (FIN) AF: 0.952 AC: 10112 AN: 10620

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63172 AN: 68016

Other (OTH) AF: 0.930 AC: 1961 AN: 2108

Alfa AF: 0.936 Hom.: 8283

Bravo AF: 0.935

Asia WGS AF: 0.936 AC: 3256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.49
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs643671; hg19: chr7-17483806;