rs6448432

Positions:

• chr4-26097188-G-A
• chr4-26097188-G-T

Variant summary

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

The ENST00000637313.1(LINC02357):​n.1409-6857G>A 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 0.284 in 152,182 control chromosomes in the GnomAD database, including 6,526 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 0.28 (6526 hom., cov: 33)
• Consequence: LINC02357 ENST00000637313.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

Genes affected

LINC02357 (HGNC:53279): (long intergenic non-protein coding RNA 2357)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02357	XR_925506.3	n.1409-6857G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02357	ENST00000637313.1	n.1409-6857G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43138 AN: 152064 Hom.: 6518 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.284 AC: 43167 AN: 152182 Hom.: 6526 Cov.: 33 AF XY: 0.278 AC XY: 20659 AN XY: 74394

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.289

Alfa AF: 0.243 Hom.: 1491

Bravo AF: 0.286

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6448432; hg19: chr4-26098810;