XR_002958413.2:n.483-9016T>C

Variant names:

• chr1-189559313-T-C
• rs382645
• ENST00000758531.1:n.92+6112T>C

Variant summary

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

The XR_002958413.2(LOC105371657):​n.483-9016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,810 control chromosomes in the GnomAD database, including 19,923 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 0.51 (19923 hom., cov: 32)
• Consequence: LOC105371657 XR_002958413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 1 publications found

Genes affected

LINC01701 (HGNC:52489): (long intergenic non-protein coding RNA 1701)

LOC105371657 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758531.1. 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
	LINC01701	ENST00000758531.1		n.92+6112T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77559 AN: 151694 Hom.: 19915 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.511 AC: 77595 AN: 151810 Hom.: 19923 Cov.: 32 AF XY: 0.513 AC XY: 38063 AN XY: 74192

African (AFR) AF: 0.521 AC: 21580 AN: 41386

American (AMR) AF: 0.458 AC: 6979 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3470

East Asian (EAS) AF: 0.596 AC: 3045 AN: 5106

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6264 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34174 AN: 67914

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.500 Hom.: 9968

Bravo AF: 0.507

Asia WGS AF: 0.452 AC: 1571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.59
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs382645; hg19: chr1-189528443; COSMIC: COSV60001869;