3-169027386-C-T

Variant names:

• chr3-169027386-C-T
• rs1024830
• ENST00000650951.1:n.456-9931C>T

Variant summary

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

The ENST00000650951.1(LINC01997):​n.456-9931C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 152,140 control chromosomes in the GnomAD database, including 712 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 0.058 (712 hom., cov: 30)
• Consequence: LINC01997 ENST00000650951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

LINC01997 (HGNC:52831): (long intergenic non-protein coding RNA 1997)

ENSG00000303122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650951.1. 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
	LINC01997	ENST00000650951.1		n.456-9931C>T		intron	N/A
	ENSG00000303122	ENST00000791975.1		n.196+4273G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8758 AN: 152022 Hom.: 706 Cov.: 30

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0577 AC: 8777 AN: 152140 Hom.: 712 Cov.: 30 AF XY: 0.0612 AC XY: 4553 AN XY: 74384

African (AFR) AF: 0.0402 AC: 1670 AN: 41518

American (AMR) AF: 0.199 AC: 3044 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3466

East Asian (EAS) AF: 0.309 AC: 1593 AN: 5148

South Asian (SAS) AF: 0.109 AC: 527 AN: 4820

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0235 AC: 1596 AN: 68002

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.0479 Hom.: 828

Bravo AF: 0.0732

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.99
DANN	Benign	0.40
PhyloP100		-1.1

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: rs1024830;

hg19: chr3-168745174;