rs7683440

Variant names:

• chr4-171595534-A-G
• rs7683440
• ENST00000651666.1:n.94-12680T>C

Variant summary

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

The ENST00000651666.1(LINC02174):​n.94-12680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,146 control chromosomes in the GnomAD database, including 3,108 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 0.14 (3108 hom., cov: 32)
• Consequence: LINC02174 ENST00000651666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 0 publications found

Genes affected

LINC02174 (HGNC:53037): (long intergenic non-protein coding RNA 2174)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651666.1. 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
	LINC02174	ENST00000651666.1		n.94-12680T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20872 AN: 152028 Hom.: 3104 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.137 AC: 20911 AN: 152146 Hom.: 3108 Cov.: 32 AF XY: 0.134 AC XY: 9976 AN XY: 74362

African (AFR) AF: 0.376 AC: 15590 AN: 41464

American (AMR) AF: 0.0654 AC: 999 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5172

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4824

European-Finnish (FIN) AF: 0.0485 AC: 514 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3025 AN: 68020

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.0694 Hom.: 1451

Bravo AF: 0.150

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.58
PhyloP100		-0.21

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: rs7683440;

hg19: chr4-172516685;