16-10685884-A-C

Variant names:

• chr16-10685884-A-C
• rs2719726
• NM_144674.2:c.719+3369T>G

Variant summary

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

The NM_144674.2(TEKT5):​c.719+3369T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,752 control chromosomes in the GnomAD database, including 23,521 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 0.55 (23521 hom., cov: 30)
• Consequence: TEKT5 NM_144674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 5 publications found

Genes affected

TEKT5 (HGNC:26554): (tektin 5) Predicted to be involved in cilium assembly and cilium movement involved in cell motility. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144674.2. 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
	TEKT5	NM_144674.2	MANE Select	c.719+3369T>G		intron	N/A	NP_653275.1	Q96M29

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT5	ENST00000283025.7	TSL:1 MANE Select	c.719+3369T>G		intron	N/A	ENSP00000283025.2	Q96M29
	TEKT5	ENST00000576638.1	TSL:3	c.38+3369T>G		intron	N/A	ENSP00000458802.1	I3L1F7

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83247 AN: 151634 Hom.: 23488 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.549 AC: 83339 AN: 151752 Hom.: 23521 Cov.: 30 AF XY: 0.551 AC XY: 40856 AN XY: 74132

African (AFR) AF: 0.671 AC: 27785 AN: 41382

American (AMR) AF: 0.593 AC: 9042 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3466

East Asian (EAS) AF: 0.627 AC: 3223 AN: 5144

South Asian (SAS) AF: 0.509 AC: 2436 AN: 4782

European-Finnish (FIN) AF: 0.493 AC: 5176 AN: 10504

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32820 AN: 67924

Other (OTH) AF: 0.520 AC: 1094 AN: 2102

Alfa AF: 0.500 Hom.: 87261

Bravo AF: 0.559

Asia WGS AF: 0.561 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2719726; hg19: chr16-10779741; COSMIC: COSV51589366;