4-10725083-C-T

Position:

• chr4-10725083-C-T

Variant summary

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

The XM_011513775.3(CLNK):​c.3+9445G>A 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: CLNK XM_011513775.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

CLNK (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLNK	XM_011513775.3	c.3+9445G>A		intron_variant			XP_011512077.1
CLNK	XM_017007684.2	c.3+9445G>A		intron_variant			XP_016863173.1

Ensembl

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

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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.427

Alfa AF: 0.470 Hom.: 5267

Bravo AF: 0.426

Asia WGS AF: 0.444 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11940117; hg19: chr4-10726707;