rs7683440

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02174	ENST00000651666.1	n.94-12680T>C		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.0445

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0582 Hom.: 759

Bravo AF: 0.150

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7683440; hg19: chr4-172516685;