chr16-10694272-G-T

Variant names:

• chr16-10694272-G-T
• rs2251985
• NM_144674.2:c.564+38C>A

Variant summary

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

The NM_144674.2(TEKT5):​c.564+38C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,517,134 control chromosomes in the GnomAD database, including 222,264 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 0.57 (25595 hom., cov: 32)
  • Exomes 𝑓: 0.53 (196669 hom.)
• Consequence: TEKT5 NM_144674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.69
• Publications: 10 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 = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT5	NM_144674.2	c.564+38C>A		intron_variant	Intron 1 of 6	ENST00000283025.7	NP_653275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT5	ENST00000283025.7	c.564+38C>A		intron_variant	Intron 1 of 6	1	NM_144674.2	ENSP00000283025.2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87271 AN: 151872 Hom.: 25567 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.541

GnomAD2 exomes AF: 0.557 AC: 101500 AN: 182140 AF XY: 0.546

Gnomad AFR exome AF: 0.681

Gnomad AMR exome AF: 0.673

Gnomad ASJ exome AF: 0.425

Gnomad EAS exome AF: 0.614

Gnomad FIN exome AF: 0.559

Gnomad NFE exome AF: 0.513

Gnomad OTH exome AF: 0.520

GnomAD4 exome AF: 0.535 AC: 730153 AN: 1365144 Hom.: 196669 Cov.: 30 AF XY: 0.533 AC XY: 356252 AN XY: 668898

African (AFR) AF: 0.680 AC: 20810 AN: 30584

American (AMR) AF: 0.666 AC: 20674 AN: 31056

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 8671 AN: 20488

East Asian (EAS) AF: 0.609 AC: 23656 AN: 38824

South Asian (SAS) AF: 0.503 AC: 36095 AN: 71808

European-Finnish (FIN) AF: 0.561 AC: 25148 AN: 44844

Middle Eastern (MID) AF: 0.404 AC: 2156 AN: 5332

European-Non Finnish (NFE) AF: 0.529 AC: 563369 AN: 1065844

Other (OTH) AF: 0.525 AC: 29574 AN: 56364

GnomAD4 genome AF: 0.575 AC: 87351 AN: 151990 Hom.: 25595 Cov.: 32 AF XY: 0.576 AC XY: 42774 AN XY: 74288

African (AFR) AF: 0.677 AC: 28041 AN: 41448

American (AMR) AF: 0.609 AC: 9310 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1544 AN: 3464

East Asian (EAS) AF: 0.621 AC: 3203 AN: 5158

South Asian (SAS) AF: 0.507 AC: 2443 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5817 AN: 10538

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35418 AN: 67970

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.471 Hom.: 3089

Bravo AF: 0.581

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.51
PhyloP100		-3.7
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: rs2251985; hg19: chr16-10788129; COSMIC: COSV51586882; COSMIC: COSV51586882;