rs6448432

Variant names:

• chr4-26097188-G-A
• rs6448432
• ENST00000637313.1:n.1409-6857G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000733074.1(LINC02357):​n.408-6857G>A variant causes a intron 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 ENST00000733074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733074.1. 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
	LINC02357	ENST00000637313.1	TSL:5	n.1409-6857G>A		intron	N/A
	LINC02357	ENST00000733074.1		n.408-6857G>A		intron	N/A
	LINC02357	ENST00000733075.1		n.372-6857G>A		intron	N/A

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

African (AFR) AF: 0.325 AC: 13498 AN: 41526

American (AMR) AF: 0.248 AC: 3788 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3464

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5188

South Asian (SAS) AF: 0.135 AC: 652 AN: 4826

European-Finnish (FIN) AF: 0.273 AC: 2885 AN: 10578

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20405 AN: 67998

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.259 Hom.: 3038

Bravo AF: 0.286

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.50
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6448432; hg19: chr4-26098810;