chr4-10735030-T-C

Variant names:

• chr4-10735030-T-C
• rs6831297
• ENST00000720792.1:n.422+172T>C

Variant summary

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

The ENST00000720792.1(LINC02498):​n.422+172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,082 control chromosomes in the GnomAD database, including 11,475 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 0.36 (11475 hom., cov: 33)
• Consequence: LINC02498 ENST00000720792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 publications found

Genes affected

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

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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.422+172T>C		intron	N/A
	LINC02498	ENST00000720793.1		n.323+172T>C		intron	N/A
	LINC02498	ENST00000720794.1		n.399+172T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54272 AN: 151966 Hom.: 11430 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.357 AC: 54359 AN: 152082 Hom.: 11475 Cov.: 33 AF XY: 0.356 AC XY: 26475 AN XY: 74356

African (AFR) AF: 0.597 AC: 24738 AN: 41456

American (AMR) AF: 0.250 AC: 3819 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1775 AN: 5174

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3240 AN: 10578

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17356 AN: 67978

Other (OTH) AF: 0.356 AC: 749 AN: 2106

Alfa AF: 0.308 Hom.: 1396

Bravo AF: 0.361

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-1.2

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: rs6831297;

hg19: chr4-10736654;