5-6879865-T-C

Variant names:

• chr5-6879865-T-C
• rs275437
• ENST00000510622.1:n.192-6561T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188250.1(LOC105374642):​n.401-6561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,082 control chromosomes in the GnomAD database, including 24,378 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 0.56 (24378 hom., cov: 32)
• Consequence: LOC105374642 NR_188250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

Genes affected

ENSG00000250060 (HGNC:):

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374642	NR_188250.1	n.401-6561T>C		intron_variant	Intron 2 of 2
LOC105374642	NR_188251.1	n.285-6561T>C		intron_variant	Intron 1 of 1
LOC105374642	NR_188252.1	n.204-6561T>C		intron_variant	Intron 2 of 2
LOC105374642	NR_188253.1	n.368-6561T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250060	ENST00000510622.1	n.192-6561T>C		intron_variant	Intron 2 of 2	5
LINC02196	ENST00000648809.1	n.172+40234T>C		intron_variant	Intron 1 of 5
ENSG00000250060	ENST00000655466.1	n.361-6561T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.559 AC: 85018 AN: 151964 Hom.: 24366 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.559 AC: 85065 AN: 152082 Hom.: 24378 Cov.: 32 AF XY: 0.554 AC XY: 41219 AN XY: 74340

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.585

Alfa AF: 0.563 Hom.: 7647

Bravo AF: 0.557

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275437; hg19: chr5-6879978;