rs7683440

chr4-171595534-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02174	ENST00000651666.1	n.94-12680T>C		intron_variant, non_coding_transcript_variant

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;