4-10725083-C-T

Variant names:

• chr4-10725083-C-T
• rs11940117
• XM_011513775.3:c.3+9445G>A

Variant summary

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

The ENST00000720792.1(LINC02498):​n.164+9076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,738 control chromosomes in the GnomAD database, including 15,073 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 0.43 (15073 hom., cov: 31)
• Consequence: LINC02498 ENST00000720792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 6 publications found

Genes affected

CLNK (HGNC:17438): (cytokine dependent hematopoietic cell linker) MIST is a member of the SLP76 family of adaptors (see LCP2, MIM 601603; BLNK, MIM 604515). MIST plays a role in the regulation of immunoreceptor signaling, including PLC-gamma (PLCG1; MIM 172420)-mediated B cell antigen receptor (BCR) signaling and FC-epsilon R1 (see FCER1A, MIM 147140)-mediated mast cell degranulation (Cao et al., 1999 [PubMed 10562326]; Goitsuka et al., 2000, 2001 [PubMed 10744659] [PubMed 11463797]).[supplied by OMIM, Mar 2008]

LINC02498 (HGNC:53483): (long intergenic non-protein coding RNA 2498)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720792.1. 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
	LINC02498	ENST00000720792.1		n.164+9076C>T		intron	N/A
	LINC02498	ENST00000720793.1		n.65+9076C>T		intron	N/A
	LINC02498	ENST00000720794.1		n.141+9076C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65658 AN: 151618 Hom.: 15060 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.433 AC: 65680 AN: 151738 Hom.: 15073 Cov.: 31 AF XY: 0.442 AC XY: 32794 AN XY: 74150

African (AFR) AF: 0.266 AC: 10963 AN: 41282

American (AMR) AF: 0.523 AC: 7976 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2744 AN: 5160

South Asian (SAS) AF: 0.477 AC: 2293 AN: 4810

European-Finnish (FIN) AF: 0.551 AC: 5805 AN: 10534

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32645 AN: 67920

Other (OTH) AF: 0.427 AC: 894 AN: 2096

Alfa AF: 0.463 Hom.: 6472

Bravo AF: 0.426

Asia WGS AF: 0.444 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.35
PhyloP100		-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11940117;

hg19: chr4-10726707;