4-10725229-C-T

Variant names:

• chr4-10725229-C-T
• rs16872571
• XM_011513775.3:c.3+9299G>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+9222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 137,804 control chromosomes in the GnomAD database, including 6,697 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 0.32 (6697 hom., cov: 31)
• Consequence: LINC02498 ENST00000720792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 23 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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+9222C>T		intron	N/A
	LINC02498	ENST00000720793.1		n.65+9222C>T		intron	N/A
	LINC02498	ENST00000720794.1		n.141+9222C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 44598 AN: 137706 Hom.: 6689 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.324 AC: 44635 AN: 137804 Hom.: 6697 Cov.: 31 AF XY: 0.318 AC XY: 21325 AN XY: 67134

African (AFR) AF: 0.354 AC: 13456 AN: 37964

American (AMR) AF: 0.314 AC: 4466 AN: 14232

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1150 AN: 3254

East Asian (EAS) AF: 0.243 AC: 1061 AN: 4360

South Asian (SAS) AF: 0.249 AC: 986 AN: 3952

European-Finnish (FIN) AF: 0.276 AC: 2572 AN: 9324

Middle Eastern (MID) AF: 0.162 AC: 42 AN: 260

European-Non Finnish (NFE) AF: 0.325 AC: 20071 AN: 61716

Other (OTH) AF: 0.329 AC: 624 AN: 1898

Alfa AF: 0.479 Hom.: 74053

Bravo AF: 0.300

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16872571; hg19: chr4-10726853;