7-153403101-C-T

Variant names:

• chr7-153403101-C-T
• rs6965505
• ENST00000453187.2:n.474+2391G>A

Variant summary

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

The ENST00000453187.2(LINC01287):​n.474+2391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,098 control chromosomes in the GnomAD database, including 10,680 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 0.36 (10680 hom., cov: 33)
• Consequence: LINC01287 ENST00000453187.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 publications found

Genes affected

LINC01287 (HGNC:50351): (long intergenic non-protein coding RNA 1287)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453187.2. 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
	LINC01287	NR_125776.1		n.380+2391G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01287	ENST00000453187.2	TSL:3	n.474+2391G>A		intron	N/A
	LINC01287	ENST00000454441.2	TSL:5	n.380+2391G>A		intron	N/A
	LINC01287	ENST00000647863.1		n.476+2391G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54080 AN: 151980 Hom.: 10667 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.356 AC: 54097 AN: 152098 Hom.: 10680 Cov.: 33 AF XY: 0.348 AC XY: 25870 AN XY: 74342

African (AFR) AF: 0.191 AC: 7921 AN: 41504

American (AMR) AF: 0.339 AC: 5181 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1549 AN: 5162

South Asian (SAS) AF: 0.368 AC: 1775 AN: 4820

European-Finnish (FIN) AF: 0.319 AC: 3375 AN: 10564

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31194 AN: 67960

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.385 Hom.: 1593

Bravo AF: 0.350

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs6965505; hg19: chr7-153100186;