rs643671

Positions:

• chr7-17444182-T-A
• chr7-17444182-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110014.1(LINC02888):​n.140-4699T>A variant causes a intron, non coding transcript 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: LINC02888 NR_110014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804

Genes affected

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

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

LOC105375172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02888	NR_110014.1	n.140-4699T>A		intron_variant, non_coding_transcript_variant
LOC105375172	XR_001745108.1	n.1895-7949A>T		intron_variant, non_coding_transcript_variant
LINC02888	NR_110015.1	n.140-6813T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02888	ENST00000419463.1	n.190-4699T>A		intron_variant, non_coding_transcript_variant		2
LINC02889	ENST00000636929.1	n.1312+12500A>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.930

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs643671; hg19: chr7-17483806;