chr4-10754433-G-A

Position:

• chr4-10754433-G-A

Variant summary

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

The XR_925377.3(LINC02498):​n.632-4661G>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 0.292 in 151,944 control chromosomes in the GnomAD database, including 7,143 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 0.29 (7143 hom., cov: 32)
• Consequence: LINC02498 XR_925377.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

LINC02498 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02498	XR_925377.3	n.632-4661G>A		intron_variant, non_coding_transcript_variant
LINC02498	XR_925378.3	n.632-4661G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44381 AN: 151826 Hom.: 7114 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.292 AC: 44442 AN: 151944 Hom.: 7143 Cov.: 32 AF XY: 0.293 AC XY: 21761 AN XY: 74216

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.299

Alfa AF: 0.255 Hom.: 876

Bravo AF: 0.290

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.035
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516211; hg19: chr4-10756057;